I cant seam to get any sound out of the left rear rca connection, the connection from the RCA connector to the amp is fine since I get sound if I plug one of the other connectors into it. Also the connection on the harness to the wire seems ok (even though I had the remote amp and power wire come out on me whjch I fixed the best I could), although I do not have a device to physically check that connection.
Are there any known problems that have come up like this, it almost seems like its a problem with the player if it isnt in the connection and if so is there anythign I can do about it? I"m running the beta 11 if that might have something to do with it.

Even though it's not all the way pulled out, odds are it's a variation on this. Especially since you already had a couple of other wires pull out. Unscrew the connector from the docking cradle and inspect it carefully, and do the procedure in the video there.