After a lengthy conversation with MagicTux, unless it does turn up that mtgox has been hacked, neither of us can figure out what happened. Its obviously not me and I didn't fall for a phishing expedition, and Im pretty sure its not on his end. His description of security on the new post-hack mtgox is pretty decent. Its not perfect, but he has gone to great lengths to prevent a repeat.
Your compromise may be linked to a huge mystery that was never solved during the MtGox hack of June 19, 2011:
many supremely strong passwords were cracked, but no one, not even Mark Karpelès, knows how it happened. One of the theories I posted in this comment is that the MtGox infrastructure has been deeply compromised, and attackers still have access to it. (I hope this is not true.)
If not that, I know that we, security-conscious people, like to think it would never happen to us, but you may have fallen to sophisticated targeted attack. There are occurrences of paranoiac security guys who do get compromised. For example even if your Linux workstation is relatively secure and updated, all it would take to compromise you is a Flash 0-day and to entice you to visit a malicious site. You may say you won't fall for it, but you do it all the time: you hang in #bitcoin-mining, someone posts a URL, you click on it. Bam! User-level X11 keylogger now running on your fully patched Linux machine. Flash is by far the scariest client-side attack vector these days...