First I think we need to Repair any Directory problems.
"Try Disk Utility
1. Insert the Mac OS X Install disc, then restart the computer while holding the C key.
2. When your computer finishes starting up from the disc, choose Disk Utility from the Installer menu. (In Mac OS X 10.4 or later, you must select your language first.)
Important: Do not click Continue in the first screen of the Installer. If you do, you must restart from the disc again to access Disk Utility.
3. Click the First Aid tab.
4. Select your Mac OS X volume.
5. Click Repair. Disk Utility checks and repairs the disk."
http://docs.info.apple.com/article.html?artnum=106214
Then try a Safe Boot, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, reboot when it completes.
(Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive.)
On Mail...
First Quit Mail, then I'd backup these two Mail folders, by right clicking on them in the Finder, then choose Archive/Compress.
Users/YourUserName/Library/Mail
Users/YourUserName/Library/Mail Downloads
(Could be a different folder here if you chose such in Mail Prefs)
Right click on that Mail folder, choose archive, you'll get everything in the folder, and the folder itself in a file called Mail.zip, move it to a safe place, same for the Mail Downloads folder... only the plist is separate.
/Users/YourUserName/Library/Preferences/com.apple.mail.plist
