So you have 1 4GB RAM stick in slot 2 then? The board was designed to have slot 1 populated. The manual states that memory needs to be in slot 1 in order for Cool'n'Quiet (AMD CPU Overheat protection) to function properly. Since you are operating on (presumed) faulty hardware, it may be difficult to say exactly why you have seen a change in the reported memory. It might have to do with an internal fault, a voltage difference, the memory failing, or an electrical difference within the system when using RAM in a different slot than designed especially if you have anything extra on the PCI bus.
I tried to see if there was a Spec sheet for that board, but there doesn't seem to be one available. Without having additional hardware for testing, and another of the same board with the same BIOS version, you may never know for sure.