When I right-click a Trash folder and choose "Empty Trash", the trash folder disappears. Then I can no longer delete messages in that account. Apparently there is no place for them to go. The same behavior happens in Email Accts, RSS Accts, and Local Folders.
If I restart TB then the Trash folder appears again, complete with all items that were supposed to have been deleted.
Thunderbird 2.0.0.9 (Portable Apps)
Windows XP Pro SP2
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This entry in MozillaZine refers to the problem (2nd bullet under Related Problems).
http://kb.mozillazine.org/Nstmp_folders
Unfortunately they only provide a partial solution. Restarting TB will indeed restore the Trash Folder, but all the trash is still in it.
Just today I began to experience the "nstmp" folder problem which is the central point of the MozillaZine article. With some effort I was able to defeat that problem, but the Empty Trash problem lives on.