Random apps fail to respond, can't use force quit - weird!

Question

Hi.
Background = My G5 had occasional weird behaviour for a long time, usually ending in failing disk verification and making me run disk repair from startup DVD to fix it. After a few months of this I got tired and cloned my disk, erased the HD, reinstalled Tiger and copied the files back.
What happened? I got a new problem. Now, apps (seemingly chosen at random) suddenly quit themselves, leaving their windows open on screen and impossible to select or make active. Force quit doesn't work because the app isn't running (despite its presence). Only option is to restart/log out and log in again. The apps this affects have included Photoshop, iCal, Mail, Safari, Preview, Word and today, Finder.
Today's experience is particularly galling since I've just spent about 8 hours creating a new user account and manually moving all my settings across (because I thought maybe it was something in there, or the permissions or something). Now my screen is covered with Finder windows that can't be got rid of.
Please, someone?
Thanks in advance,
Jason
PS This is a standard user account, clean install of Tiger about 10 days old. Problem doesn't occur on the Powerbook.
Dual G5 2.5Ghz, Powerbook G4 1.33Ghz, iPod 40GB, 250GB external drive   Mac OS X (10.4.7)  

Answer 1

So, assuming it's a software conflict, how can I
start homing in on it?
First restart and hold down the shift key when you get the bong. This will start you up in Safe Mode which turns off all third party software additions as well as additional fonts. It will also trash some font caches so if you did anything in Font Book you will need to redo them.
Then just use it for awhile and see how it functions, if no problems then you know it is something that got turned off. A couple of things won't function in Safe Mode but I don't remember what they are, do some searching in Apple's Knowledge Base here and find out for sure.
Open your system preferences and go to Accounts/user/Login Items and see what's there. All of them will have been turned off so write down what is in there or take a screen shot so you have a record of what they all were, then delete them (leave any Apple ones there). When your system restarts you will just need to see how it functions then add each of those back one at a time until things go wrong.
Also, if any apps you installed added a preference pane they will now be missing but will come back when you restart normally. If the problem happens again right away then it could likely be a preference pane. Also open up Font Book and see what fonts it is using and not using and keep track of that. It could be a damaged font, too. The Safe Mode turns off all but the basic system fonts.
One note, it sounds like what ever is wrong has already caused some directory damage so you will need to repair that before doing any of the above. If you have Disk Warrior that is the best directory repair to use, if not start up off of your install disk and do repairs using the Disk Utility that is on the DVD.
It would be a good idea to go here:
http://www.thexlab.com/faqs/durepairfns.html
Browse Dr. Smoke's X-Lab FAQS and you will find all I said above but explained better and with more detail, and probably a few other things I forgot. He has lots of free info here including how to go about finding a software conflict.
Kevin