I've had been anxiously awaiting the .5 update for Jag-wire for a while so I snappily installed it the other day as soon as it popped up in Software Update.
Today I started to have some problems. First off xplanet was not updating my background image properly. I use a couple scripts I wrote to download current cloud maps and draw the Earth as my desktop background. When trying to update my background this morning the wget part of the xplanet script worked fine but xplanet would crap out and do nothing for me. I checked the permissions and everything seemed in order (xplanet was executable by my UID). Then later Arts & Letters daily started to crash Safari (v60) which it had never done before. The display pane of System Preferences would also detach from the window into its own little control-less window. Switching panes would make the wndow disappear and SP work properly but the Display pane would keep pulling that little stunt. I logged out and back in to no avail.
Instead of hassle with the combo updater I used Disk Utility to repair disk permissions and updated prebinding. Then once I rebooted I ran periodic daily weekly monthly.
Both the problem with xplanet and Safari have disappeared and upon checking the display pane separation issue is also resolved. I didn't run into other problems but I'm sure some of you have.
The moral of the story is this, if you've run the 2.4-2.5 update or even the combo update, run Repair Permissions in DU and update prebinding on /. I ran periodic because my Powerbook is asleep most of the times cron jobs run and I didn't want to wait for anacron to cycle so that step is optional. If you've having problems run Disk Utility and update prebinding.