Yes that sounds painful, thanks very much for taking the extra time to post! The longer bits were probably the result of infrequent virtual machine use. It is a shame we don't have a real mac solution. Here are a few things that might help in the future:-

Compile

The Arduino compiler is entirely unrelated to any Atmel configuration. Therefore if you have a compile error there is no need to review your Atmel installation

Debugger

There are notes on the "downloads" pages, home page, top of the forum posts and in the new releases section of the forum to explain that the debugger is now activated by default from v1309.4. You can revert to project by project enabling of debug why setting Auto Enable Debug to False in the Tools Options. Or use the "debug>start without debugging/deploy" commands.

I suspect the error you were getting was a "corrupted" Arduino core.

The debug compile uses standard Arduino syntax so a debug compile problem can only be invalid breakpoint settings, project source redefining the debug port or arduino core data types or a corrupted core.

In the case of a corrupted core it would also be a good idea to click "Build>Clean Solution" after fixing the error just to ensure that cached compiler cores are updated. Clearing the VM AppData folder is what the "clean" does so your guessing probably helped

Latest Release - 1309.11

There has been 1309.11 released in the last few days which related to the underlying config changes of the latest Arduino 1.5.3 version of Arduino (released a week ago). It depends which version of arduino you had installed previously. It won't have been 1.5.3.

1309.11 polishes off the changes that allow Visual Micro to now support all Arduino versions even the new 1.5.3 with a new optional library format. It also fixes issues for windows xp users (not sure if that is you). 

Releases take a few days to appear in the Atmel Gallery so our downloads site is always the most current.

New Release Notifications, Tips, fixes and additions lists

All patches are notified by email by subscribing to our download site or subscribing or viewing the "new releases" forum board. 

There is also a popup dialog that appears when a new visual micro major version is available

The list of recent changes list and current release version number is always shown on our downloads site by clicking the DOWNLOADS (plural) button. 

On the DOWNLOADS page you will also see every previous version of visual micro. The Visual Micro version is also displayed on the Atmel Studio gallery page.

License Key

The early versions of Visual Micro that supported License keys suffered from the Licence key registration becoming reset, this was especially so for Virtual Machines. Clearing  the VM registry or re-installing on a Virtual Machine might well be subject to requiring the key to be re-entered and might also cause the need to contact visualmicro.com for a key reset. More testing is needed in this area sorry.

I hope that I can save you some future hassle by saying that, other than the "Locations" section of the Visual Micro registry everything in the vm registry is unimportant. The "locations" section simply points to where Arduino is installed.

In terms of program files the installer only installs files in "program files/visual micro..." and does not alter any Atmel or Arduino files. So the dlls in the vm program folder are all there is to Visual Micro.

There was a problem with 1309.4, the installer didn't update one of the Visual Micro dlls. Requiring uninstall and re-install.

The safest and easiest way to uninstall Visual Micro is "Add or Remove Programs>Visual Micro for Arduino"

Summary

I know half the stuff above is not relevant to you, it just seems like a good time to include it in a thread as a reminder for others.

Appreciate the post, it will no doubt be useful to others. Sorry for the major changes in the product recently however  it is mainly due to Arduino