Since I upgraded Thunderbird to version 3.xx a little while ago, it automatically configured my Gmail account to IMAP. While there are benefits to IMAP, one of the disadvantages is that I cannot receive the same email twice from two different clients. I have Thunderbird at work with my Gmail account setup, and I also have Thunderbird at home where my Gmail account is also setup. Whichever email client receives the message using IMAP first, gets it. There is no “leave messages on server” option with IMAP. The solution is to go back to using POP, but with Thunderbird 3.0, that was even a chore to figure out. These two great resources explain how to do just that.
Also, be sure to setup your Gmail accounts and use the recent mode http://mail.google.com/support/bin/answer.py?hl=en&answer=47948