In testing something else out, I am getting the same symptoms. I filed Issue #22:
https://github.com/gavinandresen/bitcoin-git/issues/issue/22
https://github.com/gavinandresen/bitcoin-git/issues/issue/22
Update:
I was able to download the block chain and the transaction showed up with over 400 confirmations.
Thinking about this problem, it would be nice if there was an option to recheck the blocks that have been downloaded after a wallet restore instead of using up so much network bandwidth.
Better yet, a fully automated wallet backup and encryption / password protection would be nice for the average user.
I got a little nervous when I thought my whole savings account may be lost.