Ok, starting a new thread for this.
VM 1.1407.10
Arduino 1.5.7
Arduino 1.0.5 r2
Arduino 1.0.6
VS 2008
Win 8.1

Using V1x IDE's - no boards available in either VS2008 or Atmel 6.2
ide 1.5.7 with 1.5x is ok.

Shots of paths as requested.

Thanks very much for all the effort.

Please try/consider these things one by one to see if this makes a difference or identifies the issue.

1) Ensure that the arduino.exe is in the folders you have specified and not in a second level folder below. Otherwise alter the path to the lower folder where the .exe is. The arduino zips often duplicate the folder structure.

2) Clear the sketchbook location and click OK. This will test if an invalid user library or custom hardware definition is throwing things out (in which case this would be a bug in vm)

3) Click tools>visual micro>reset user interface

4) Switch on "tools>options>visual micro>user interface>trace". re-start the ide and post the output

EDIT: also confirm you have run the 1.0.5 or 1.0.6 ide at least once.

Thanks again

Hi Tim,
ok here we go 
Your checklist -
1- yes exe is where it should be
2- clearing sketchbook location makes no difference
3- reset use interface makes no difference

4 - with trace on -

1.0.5r2
105 r2
Configuration      Cygwin: C:\cygwin64
Application      Begin
Status      Application - Extenders Created
Status      AddinKickOff - Setup temp commands required
Status      AddinKickOff - Command event obtained
Status      Launched - Mcu Init
Info      MyVisualMicro location C:\Users\Joe\Documents\Visual Micro
Status      Unable to select the current application
System.NullReferenceException: Object reference not set to an instance of an object.
   at processing.app.MCUApplication.get_runtimeBoardsList()
   at processing.app.SketchBase.setCurrentMcuApp(String sAppName)
Status      Available application configuations =  7
Status      Launched. Application configurations loaded = 7
Create UI command items      Begin
CreateCommandBarItems      Begin AddinVer=1.1407.10
Adding      Debug status button to toolbar: Ports
Get Bar      Help
Get Bar      Tools
Create Bar      Tools>Arduino
Adding      Tools>Ports
Adding      Tools>Other Ports
Get      CustomToolBarObjects
Adding      UI Menu-Board-Items
Adding      UI Menu-SerialPort-Items
Adding      Creating project menu libraries for platform
Adding      Tools-and-libraries-menu-begin
Adding      Libraries-menu-cleared
Adding      ToolBar-Tools-Menu-Caption-Error
Adding      Lib-user-begin
Adding      Lib-user-cleared
Create UI command items      End
Launch      Complete
Status      Usb or network device connect/disconnect detected
Status      Usb or network device connect/disconnect detected
Status      Usb or network device connect/disconnect detected

the usb errors are in time with 2 popup error boxes - 1 after the other

error adding network port menu item com6-
and
error adding network port menu item com7-

these repeat apx every 5 seconds -
Note - these ports are bt ports - there is a known slowness issue in the menus and a dll to fix it for v 1.x - I did not use it on this - but - I did yesterday.

106

Configuration      Cygwin: C:\cygwin64
Application      Begin
Status      Application - Extenders Created
Status      AddinKickOff - Setup temp commands required
Status      AddinKickOff - Command event obtained
Status      Launched - Mcu Init
Info      MyVisualMicro location C:\Users\Joe\Documents\Visual Micro
Status      Unable to select the current application
System.NullReferenceException: Object reference not set to an instance of an object.
   at processing.app.MCUApplication.get_runtimeBoardsList()
   at processing.app.SketchBase.setCurrentMcuApp(String sAppName)
Status      Available application configuations =  7
Status      Launched. Application configurations loaded = 7
Create UI command items      Begin
CreateCommandBarItems      Begin AddinVer=1.1407.10
Adding      Debug status button to toolbar: Ports
Get Bar      Help
Get Bar      Tools
Create Bar      Tools>Arduino
Adding      Tools>Ports
Adding      Tools>Other Ports
Get      CustomToolBarObjects
Adding      UI Menu-Board-Items
Adding      UI Menu-SerialPort-Items
Adding      Creating project menu libraries for platform
Status      Usb or network device connect/disconnect detected
Status      Usb or network device connect/disconnect detected
Status      Usb or network device connect/disconnect detected

Same as 1.05r2 for comm port errors

1.5.7

Configuration      Cygwin: C:\cygwin64
Application      Begin
Status      Application - Extenders Created
Status      AddinKickOff - Setup temp commands required
Status      AddinKickOff - Command event obtained
Status      Launched - Mcu Init
Info      MyVisualMicro location C:\Users\Joe\Documents\Visual Micro
Status      Available application configuations =  7
Status      Launched. Application configurations loaded = 7
Create UI command items      Begin
CreateCommandBarItems      Begin AddinVer=1.1407.10
Adding      Debug status button to toolbar: Ports
Get Bar      Help
Get Bar      Tools
Create Bar      Tools>Arduino
Adding      Tools>Ports
Adding      Tools>Other Ports
Get      CustomToolBarObjects
Adding      UI Menu-Board-Items
Adding      UI Menu-SerialPort-Items
Adding      Creating project menu libraries for platform
Adding      Tools-and-libraries-menu-begin
Adding      Libraries-menu-cleared
Task      libs-get-for-ide
Adding      Lib-core: EEPROM
Adding      Lib-core: SoftwareSerial
Adding      Lib-core: SPI
Adding      Lib-core: Wire
Adding      Lib-core: Bridge
Adding      Lib-core: Esplora
Adding      Lib-core: Ethernet
Adding      Lib-core: Firmata
Adding      Lib-core: GSM
Adding      Lib-core: LiquidCrystal
Adding      Lib-core: RobotIRremote
Adding      Lib-core: Robot_Control
Adding      Lib-core: Robot_Motor
Adding      Lib-core: SD
Adding      Lib-core: Servo
Adding      Lib-core: SpacebrewYun
Adding      Lib-core: Stepper
Adding      Lib-core: Temboo
Adding      Lib-core: TFT
Adding      Lib-core: WiFi
Adding      Lib-user-begin
Adding      Lib-user-cleared
Task      libs-get-for-user
Adding      Lib-user: AC_Fence
Adding      Lib-user: AC_PID
Adding      Lib-user: AC_Sprayer
Adding      Lib-user: AC_WPNav
Adding      Lib-user: AD7746
Adding      Lib-user: ADS1115
Adding      Lib-user: ADXL345
Adding      Lib-user: adxl345driver
Adding      Lib-user: AK8975
Adding      Lib-user: APM_Control
Adding      Lib-user: APM_OBC
Adding      Lib-user: APM_PI
Adding      Lib-user: AP_ADC
Adding      Lib-user: AP_ADC_AnalogSource
Adding      Lib-user: AP_AHRS
Adding      Lib-user: AP_Airspeed
Adding      Lib-user: AP_Baro
Adding      Lib-user: AP_BattMonitor
Adding      Lib-user: AP_Buffer
Adding      Lib-user: AP_Camera
Adding      Lib-user: AP_Common
Adding      Lib-user: AP_Compass
Adding      Lib-user: AP_Curve
Adding      Lib-user: AP_Declination
Adding      Lib-user: AP_GPS
Adding      Lib-user: AP_HAL
Adding      Lib-user: AP_HAL_AVR
Adding      Lib-user: AP_HAL_AVR_SITL
Adding      Lib-user: AP_HAL_Empty
Adding      Lib-user: AP_HAL_FLYMAPLE
Adding      Lib-user: AP_HAL_Linux
Adding      Lib-user: AP_HAL_MPNG
Adding      Lib-user: AP_HAL_PX4
Adding      Lib-user: AP_InertialNav
Adding      Lib-user: AP_InertialSensor
Adding      Lib-user: AP_L1_Control
Adding      Lib-user: AP_Limits
Adding      Lib-user: AP_Math
Adding      Lib-user: AP_Menu
Adding      Lib-user: AP_Motors
Adding      Lib-user: AP_Mount
Adding      Lib-user: AP_Navigation
Adding      Lib-user: AP_Notify
Adding      Lib-user: AP_OpticalFlow
Adding      Lib-user: AP_Param
Adding      Lib-user: AP_PerfMon
Adding      Lib-user: AP_Progmem
Adding      Lib-user: AP_RangeFinder
Adding      Lib-user: AP_RCMapper
Adding      Lib-user: AP_Relay
Adding      Lib-user: AP_Scheduler
Adding      Lib-user: AP_SpdHgtControl
Adding      Lib-user: AP_TECS
Adding      Lib-user: AP_Vehicle
Adding      Lib-user: BMA150
Adding      Lib-user: bma180
Adding      Lib-user: BMP085
Adding      Lib-user: bmp085driver
Adding      Lib-user: ByteBuffer
Adding      Lib-user: DataFlash
Adding      Lib-user: DebugUtils
Adding      Lib-user: doc
Adding      Lib-user: DS1307
Adding      Lib-user: Filter
Adding      Lib-user: FreeIMU
Adding      Lib-user: GCS_Console
Adding      Lib-user: GCS_MAVLink
Adding      Lib-user: HMC5843
Adding      Lib-user: HMC5883L
Adding      Lib-user: HMC5883LArduinoV4
Adding      Lib-user: HMC58X3
Adding      Lib-user: I2Cdev
Adding      Lib-user: IAQ2000
Adding      Lib-user: ITG3200
Adding      Lib-user: itg3200filv05
Adding      Lib-user: L3G4200D
Adding      Lib-user: LM73
Adding      Lib-user: memcheck
Adding      Lib-user: MemoryFree
Adding      Lib-user: MPR121
Adding      Lib-user: MPU6050
Adding      Lib-user: MPU6050_calibration
Adding      Lib-user: MPU60X0
Adding      Lib-user: MS561101BA
Adding      Lib-user: PID
Adding      Lib-user: PinChangeInt
Adding      Lib-user: RCArduinoFastLib
Adding      Lib-user: RC_Channel
Adding      Lib-user: SITL
Adding      Lib-user: SSD1308
Adding      Lib-user: TCA6424A
Adding      Lib-user: Timer1
Adding      Lib-user: TimerOnemaster
Adding      Lib-user: _Stub
Create UI command items      End
Launch      Complete

Joe

after running ides once 
1.0.5 r2
Configuration      Cygwin: C:\cygwin64

I dont know how the cygwin path got in there ? - I didnt add it - but I did download cygwin64 yesterday to try to help with the cygwin errors.
Anyway - it is gone now - no difference...
Tried the friendly ports list and menus. - no diffference.

Link to extremely slow Arduino 1x with bluetooth serial ports fix -http://www.hobbyist.co.nz/?q=slow-response-arduino-ide-in-windows

Yes good point. It might be that. I'm sure Visual Micro creates that folder but sounds like doesn't report a permissions problem. try creating the folder and re-starting the ide.

Thanks for the link to the serial fix. I forgot to tell you to switch off "Network Discovery" in "tools>Options>visual mciro>communications"

Thanks

Good, the folder is used if it exists otherwise not and is not the problem.

Please export your registry key HK_CURRENT_USER\Software\Visual Micro and email to info[at]visualmicro.com

Thanks

I've replied. We need to rename the extension of the .reg will be blocked. Or put in a zip

Thanks

No problem.

It all looks okay. Never heard of this error before. Maybe try running the id as admin to see if it is a permissions issue  of some sort.

Sorry can't think what else to recommend at the moment although i can add some extra error info to find the issue. Will take a week or so I am afraid.