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"For example, Adobe Illustrator is hanging on me every few minutes"
Stop using crap.
"For some reason even the systray becomes borked, because of it."
Shall I repeat?
"In Vista the application won't be able to do that. In my example AI wouldn't be able to bork systray or the AI window itself, but it would still appear hung. "
So because those programs are terrible coded and your favourite OS is a mess this is a actually a feature? Wouldn't be more smart to make programs better? Yeah,
I know, redesigning a whole OS and break compatibility
with all those crapy apps is not an option.