This seems to have started happening with the 10.4.10 update, but I
had a bad crash and had to do some file system repair about the same
time so I attacked that first, then followed up on some reported
problems I'd googled in other applications that I was using, and it
took me a while to narrow things down to APE and then MOAB 1.1.

With MOAB 1.1 enabled my computer can take several minutes to 1/4 an
hour to let me log in, and applications periodically slow down and
almost lock up. You can see a delay from 12:58:48 to 12:59:52 between
SideTrack noticing that the UID had changed and the first message from
loginwindow, and the last message during login doesn't come until
13:01:06.

Oct 30 12:58:48 Majora /System/Library/Extensions/SideTrack.kext/
Contents/Resources/sidetrackd: SideTrackConfigPush: Setting driver to
configuration for UID 501.
2007-10-30 12:59:52 -0500
2007-10-30 12:59:52.936 loginwindow[59] FSResolveAliasWithMountFlags
returned err = -35
...
2007-10-30 13:01:06.825 WinSwitchHelper[242] Could not get menu extra
(-4956)

After temporarily disabling APE login was pretty much instant, and
after disabling MOAB 1.1 and re-enabling APE the whole process still
completed in 20 seconds:

Oct 30 13:16:11 Majora /System/Library/Extensions/SideTrack.kext/
Contents/Resources/sidetrackd: SideTrackConfigPush: Setting driver to
configuration for UID 501.
2007-10-30 13:16:20 -0500
2007-10-30 13:16:20.377 loginwindow[390] FSResolveAliasWithMountFlags
returned err = -35
...
2007-10-30 13:16:33.649 SystemUIServer[408] Normally SSMenuExtra would
not have been loaded as a Menu Extra.

The other APE modules I'm using are ClearDock, PD Tweaker, and Unifier.