It looks like the block chain simply hasn't synced up fully for you. It usually takes a few hours to download the whole block chain and during this time the program will have inaccurate balances.

Verify your block count

Check your Bitcoind's block count with the getblockcount command and make sure it matches up with the network's block count. Heres the network block count, maintained by blockchain.info.

Make sure you're downloading blocks

If it doesn't match up, make sure your Bitcoind is atleast in the process of downloading blocks, try the command a minute later and see if it has incremented since then. If the block count stays the same number over a few minutes, it very likely that the following is your problem.

Why a server isn't downloading the block chain

Something that I've seen happen is that Bitcoind may stop downloading blocks at some point in the middle of the full chain. This happens because your server is running out of memory. Downloading the block chain is a heavy procedure because each block needs to be checked. You can remedy this by just manually moving a chain you've downloaded onto the server or get more ram (you need more than .5 gb of ram to run Bitcoind anyways). The community has the block chain available on torrent.