During my testing of Windows 7 I have had almost no issues to report, the only things that have been of notice have been third party or driver related. Then there’s the permissions bug, this bug is so elusive that hardly anybody has reported it and nobody has a solution, not even me.
Update 1: It appears that as of build 7068 this bug may have been fixed, see comments below for details.
Update 2: There are reports the bug has reappeared in the RTM build, it can also occur in Windows Vista but slightly less often.
Update, September 2 2009: It has been mentioned below that this website has a possible fix and that it can fix both Windows Vista and Windows 7. I don’t get this bug any more on any of my machines so I am unable to verify it however.