Having a socket or not is NOT going to make a difference unless the contacts are really dirty(and then it probably does not even work). But of course you can still have cold solder joints on the soldered in CPU too. But still, if pins of your CPU are not making contact the board is likely not functioning or not functioning properly.

What may make a difference is if these boards have any other differences. You are not looking at the socket here, you are looking for different ROM or other firmware for other parts or other parts themselves being different between the two boards.

Make sure you use the same RAM when you switch boards. And no extra PDS cards!