Mail corruption and system problems. Need solution.

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.
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 and listing it as a Mail problem( which it kinda is), 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

Verify/repair your disk first (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
If Disk Utility reports problems it cannot fix, even when starting up from a different disk, read the Disk Utility cannot repair the disk section of the following article for additional guidance and links to more powerful (third-party, not free) disk utilities:
Resolving Disk, Permission, and Cache Corruption
Post back with your observations.