I use and love Thunderbird on my PC. It's almost as bare bones as Mail, which is how I like it. I am still attempting to correct Mail though and will try to remove and stray "to-do's" though I can't remember making on in the past couple months.
Is it possible Mail is just freaking out from the sheer avalanche of junk mail my Nickmongo mail account creates? Every time I've lost all my settings I've had to recreate this account in Mail and it has had to redownload every bot comment nickmongo.com has ever received and then process it as Junk. The only problem with this theory is that Mail still has the same problem when I am not online, so it can't be trying to dredge up these old messages.
Thunderbird is very good on the PC. It's just that Mail is so well integrated in OS X, I don't see the point of switching to something not fully implemented (unless Mail doesn't work, or you're a freaking homebrew jerk).
Ok, here's what you're going to do. It's sketchy, but I'm handing you a solutions, so you might as well take it. Some browsing led me to this page:
http://www.macfixit.com/article.php?story=2005070807515981It has instructions on how to completely reinstall a low level Mac app with the program Pacifist. The program is shareware, but I have
acquired it here:
http://spacepiratesltd.com/dan/pacifist.zip . The ZIP contains a couple of serials. Use them for whatever you need. Maybe they will work with this application, and it would be a happy coincidence. Who knows.
Next, follow the instructions on the Macfixit page:
Insert your Mac OS X Installation CD or DVD
Launch Pacifist
Click the button "Open Mac OS X Install packages" (this option will be grayed out and inaccessible if no Mac OS X disc is present)
Simply select the desired, currently missing or unusable application and click "Install"
I tried this out on my Leopard machine (not a reinstallation, but to see if it could work) and it did! See below.

let us know if it works out for you.