I've read in several places that say to stay away from the Dothan 7xx(a) processors, but was wondering what exactly are the issues with them and what they were designed to do if they don't work with ThinkPads.

I don't think it's a problem of the 'A" designation as much as it is that the A designation Dothans also have 'C' stepping, which is known to be problematic in T4X machines. This is theorized to be due to embedded controller firmware in those machines that does not support the 'C' stepping Dothans.
http://forum.thinkpads.com/viewtopic.php?t=32165
http://en.wikipedia.org/wiki/List_of_In ... processors

Thanks. That thread was the one I needed and didn't find in my search. It looks like that's where my issue is at.

No wonder my upgrade T41 runs like a slug. I guess I'll find out for sure when the regular (non "a") Dothan shows up this week and I put it in! It'll be like getting another new machine!

Slowing your machine down with a bad CPU, $50 bucks ...getting another new machine out of the deal, priceless