Bitcoin client is still saying out of sync but I'm pretty sure blockchain is done downloading. That's what I don't get. I can find the transaction, see my bitcoins sitting there, but they're not in my wallet.
Nope. If it's saying out of sync then the client is sure the blockchain isn't fully downloaded, or do you think you know about it better than the client and the network? lol
It may have happened that it hanged. But if it did your only way out is to delete the blockchain files and start over.
How many connections to the network does it have? How many blocks did it download?
Just hover your mouse pointer above the icons on the bottom right corner and it will tell you what I just asked.