Well, this is driving Sneakers and I nuts. It's been a once in a while prob over the past couple of years (started before we moved!), and now it's a daily problem. I have no idea how to solve this and I sure hope someone here does.
So, Sneakers keeps a LOT of mail. Lots and lots of it - as in Gigabytes worth!

It often all sits in his IN box (hey it's his mail and his machine and his way and I keep my mouth shut - most of the time).

The problem is:
There are several hundred pieces of email that keep "downloading" from somewhere. The same ol' emails. They go back to 2005! We've trashed them and emptied trash. We've compacted folders. I've verified at our hosting site that these aren't sitting there. Yet, they show up. At first, it was once in a while (as I said) ... now it occurs every time he launches Thunderbird.
He was running a really old version of TB (1.0.something) and I forced him to upgrade to version 2.0.0.9 (20071031). That didn't fix the prob.
Disk Utility shows no issues with his drive -- in fact, now that I think about it -- this drive is new since we moved, so it's not the hardware, it has to be software related.
I figure we could create a new profile and import stuff (we could do that, yes?), but I'm concerned that that would just bring whatever it is over with the import.
I'd trash a file if I knew what to trash.
If standing on my head would fix this, I'd try it.
Sneakers is running a G4, OS 10.4.11 (but this started back in 10.x days), and TB version 2.0.0.9 (20071031).
Anyhow, I said I'd ask for help ... so here I am.