Like others here, I can't seem to kick this problem. That being said I have hope that the common elements described in this thread will help Apple track down the bug and squash it. No love in 10.6.1, but perhaps in a future update (hopefully soon).
Anyways, this post is geared towards giving a nod to Time MAchine and Time Capsule. I've been using it for a while but never had to restore anything until today. Somewhere along the line in my attempts to do away with the dupes issue, I dumped all my email from the POP Yahoo account, including Sent items. For whatever reason, they somehow didn't get caught in Trash. While I was nervous at first, I knew with TM I was covered. What I didn't know was how to go about it. I initially went more complicated than necessary and was browsing back through Finder folders from previous dates. After a quick search on the forums, I saw mention of bringing Mail up and then entering Time Machine. It couldn't have been easier to go back ito the day before the mass delete and restore them.
While this problem is still annoying, I have to give credit to TM for saving my behind.
Jeff