So, up until now I've stuck with WinAVR 20090313. Independently, I've been working on a number of projects using the UC3 line of AVR32 microcontrollers, using the AVR32 toolchain included with AVR32 Stuio. I've had no problems with these pieces of software coexisting.
But I've been handed a project that uses an XMega AVR, so I just upgraded to 20100110. The new version of WinAVR also comes with a copy of the AVR32 toolchain, and it appears that the AVR32 toolchain in WinAVR is conflicting with the toolchain in AVR32 Studio.
It is reporting an inability to locate certain tools, such as avr32program.exe. And whenever I invoke a makefile-managed build, I get Cygwin warnings relating to non-POSIX paths.
Other than using two different computers, is there anything else I can do to continue using WinAVR 20100110 for 8-bit AVR work, but use the default AVR32 Studio toolchain for AVR32 development?