Aaron, it doesn't let me log in when it misdetects the version - the join server button is disabled. If I keep refreshing it sometimes picks up the server is 1.6.1 and then the button is enabled as normal and I can connect and play fine. I have three server instances on the same server (and on my list), and it randomly detects different ones as 1.6.1 each refresh, if indeed at all.
I'm not sure if this is the same issue, but I'm getting the same problem (server reporting as version 1.3) with a 1.6.1 client and a 1.6.1 server...
One of them is Craftbukkit, so 1.5.2 and irrelevant here, but the other two are using the stock 1.6.1 (just multiple invocations of the same jar).