I'm hitting some issues too, even with the beta, when working with the ICE-50 and Mega-8535.
"ghostpoints", breakpoints that I set a long time ago, where the program will stop even though there is no breakpoint currently set there. USUALLY setting and then clearing a breakpoint there will clear. This problem comes and goes.
Sometimes on launch, studio will throw an error box that says the application requested that windows terminate it in an unusual way (? WTF?) The only cure I've found for that is to uninstall studio, delete the c:\program files\atmel directory, then re-install.
I also hit one today, where it basicaly just went nuts all of a sudden.
I was being thrown into ISRs that weren't enabled, and hitting a lot of "emulation breaked due to illegal SRAM access" in sections of the code that had nothing to do with SRAM at all! Again I had to remove and reinstall studio to cure.
These last two are relatively new, "ghostpoints" I've been fighting on and off since early 2002 or thereabouts.