System Prefs. problem. Application problems. Need advice.

Question

The problems I am having:
1) Mail will not open. It hangs, shows beach ball and stays that way. All you see is the menu-bar. Force quit will not work. Only hard reset. Activity Monitor shows the app sucking up 87-95% of processor.
2) System preferences are not staying. Specifically, my mouse preferences for scrolling, keyboard illumination, Safari address bar buttons. This gets worse if I have to do a hard reset if Mail gets launched. It can clean the whole system prefs. sometimes. (update: My 2 finger scrolling goes off even when I haven't shut down, restarted, etc. I have to go into Sys. Prefs. and recheck it)
Let me start from the beginning of the problem:
I was on a website for a real estate company. It uses an active server application that never works right with a Mac. I almost always use Safari for it. What happens is that the sever app. usually hangs and won't go to the next page. I've tried all my browsers except Opera, so, I figure I would give that a go and see if it's better. BAD IDEA! Opera 8.6 hung. It wouldn't force quit. I had to do a hard reset like , 5 times, before it would restart. After that happened is when things got bad. My system prefs. were all gone. I had to reset all that. And then, Mail just went t1t5 up. It did what I said above. Hung. So I had to figure out how I was gonna get all my mail over into Thunderbird. I backed up the HD, and luckily, through Apple forums and Google, came up with the .emlx to .mbox converter. Tedious but worked. I deleted Opera off my HD as well as Mail. I am not even gonna bother with Mail again after having to deal with Apple's stupid file format and having no way to import a back-up. Thunderbird is way better and PGP actually works on it. Scr3w Opera as well.
At this point, my biggest problem I have is that my system prefs don't always seem to stick. I need to find out which files are associated with this and fix it. I am also paranoid that something got backdoored on my system and is causing havoc. Although I doubt this happened, I would like to see if someone can look at my processes and see if anything looks abnormal. All these problems have happened with my standard account with no Admin privileges ( unless I type in the Authorization on a per instance event). My Admin account is not having problems and my other standard account is OK. So I am pretty sure it's a local problem and not associated with root.
Anyone knowledgeable with some good ideas would be appreciated. I almost never have problems. I'm kinda p155ed this happened. Luckily I could still do a back-up and was not in a recording session or anything.
You can download my Processes List in PDF at this address:
http://badapplestudio.com/actmonscreen.pdf
Sorry for the long description,but there are a lot of factors that lead up to this.
Thanks,
~sKot
1.67 G4 Pbook , 500 G4 Pbook,Dual 2.7 G5 Tower   Mac OS X (10.4.7)   Also Dell P4 for Gigasampler

Answer 1

I'm having similar problems to those described by ~scot. The apps that won't launch are (so far)
Mail
Address Book
Safari
Safari gives the spinning beach ball, but Mail and Address Book merely show the black triangle indicating they are running (though they are not.)
Force quits are fights. I haven't had to restart but I have to use the force quit menu command or the "three fingered salute" four or 5 times.
Have deleted plist for Safari but hesitated to do so for Mail and Address Books because of fear of losing more than settings - perhaps too cautious but if anyone knows of another way I would prefer that.
Rebooted from original discs and ran Disk First Aid, ran TechTool Pro and Disk Warrior to no effect. Had run Onyx for regular maintenance the week before the problems began but have not done so since.
Suggestions gratefully welcome!
ceedee
Quicksilver G4   Mac OS X (10.3.9)