WinAVR has an issue that can delete your entire PATH environment variable if you allow WinAVR to update your path and you have a lot of paths stored in that variable already (it overflows). It happened to me and others have reported it as well but it will not be fixed as WinAVR is not a supported project anymore so perhaps the Atmel AVR Toolchain can be referenced here instead?
Edited. Please let us know if that was okay or no.
--Willadams 05:53, 8 October 2014 (CDT)