Thanks very much for the supportive comments!

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I agree we should optional allow atmel project properties to be used to customize the build process but I am a little confused ...

1)
Can you confirm that you had not previously modified the Arduino core or created your own custom board that appeared in the boards list that contained the -std=gnu99 setting? I know we have ways of modifying the compile process to support this but do not recall using an Atmel Studio property.

2)
Were you previously using the Due or an Avr board? 

3)
Which version of the Arduino Ide were you using with 1310?

Sorry if this is my confusion if you confirm these things I can take another look

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We are investigating this but a solution is a long way off if it works! The problem is that Arduino does not have a debug facility that is easily accessible so normally you add serial.println() messages to the code. 

The Visual Micro debugger does a similar thing. We inject Serial statements into a temp copy of the code during compile and process the serial messages when they arrive on the computer to display "debug like" windows. When a variable is modified during debug a serial message is sent to the Arduino. The injected code checks for this at each breakpoint. Conditional breakpoint expressions and hit counters also have to be managed in the injected code for each break point.

So far we have been able to relatively reliably inject this code to the end of lines that match breakpoints in the Ide (sometimes converting single line if statements to multiline). Uggh! So as you might imagine, being able to add code to every line allowing step is currently out of reach, anything short of that (other than what we have) might be unpredictable or cause code logic to fail 

As an aside, one of our members is working on a clever system that allows us to query/update variables and registers etc without need to declare prior to compilation and upload. We should get much more detailed debugging views of the hardware and it will be more flexible. That's the current hope anyway.

Hi, thanks for the  info. I agree some more settings will be useful but for now I would like to get to the bottom of this issue.

On the machine that is working please enable "tools>options>visual micro>compiler>show build properties" and also please enable "tools>options>visual micro>compiler>verbose". Build with the setting as you want them, copy and email the output to info [at] visualmicro.com

Then do the same with the latest release.

Thanks very much