Ok, I have ZD loaded up with about 6 mailboxes, here's the problem and how to reproduce it.

  1. Repro Steps
  2. Create 1 tag for Email box #1
  3. Create 1 tag for email box #2
  4. Restart Zimbra Desktop
  5. Go into Mailbox #1, highlight an email, press t and tag an email
  6. Go into Mailbox #2, highlight and email and press t

Results: you will be presented with the tag list from email box #1 (or whichever box you used first). If you start with #2, tag something and then go to box #1 and tag something yuo will be presented with the tags from box #2.
This only happens with the keyboard shortcut, I can still access the correct tag list via right click