Quoted from grimholtz:
Is there any way to test this short of buying a new board?
Run the display test. When the test starts invert the state of the auto/manual button to stop the test. Then individually step the test by using the advance button. Note what you see. The test displays all the digits zero through nine on all the strobes then enables all the segments on each individual strobe before finally enabling each individual segment on all the strobes. Look for a pattern. It should be able to help you narrow whether it is the CPU board or the display board.