The usual suspect is a faulty optocoupler (6N138).
Perhaps this is not installed, or there are bad joints there.
i.e. The PIC sends the upload requests, therefore "MIDI Out" is working. In the normal case, it would receive the upload packets and reply with acknowledgement messages. If the PICs don't receive the packet, then they don't reply. Therefore, the most likely problem is a fault in receiving MIDI, which is probably the optocoupler or something else related to it, the resistors connected to the optocoupler.
You might want to check the following components are correct and have good joints and connectivity:
D1 (check orientation!), R5, R11 (near optocoupler), R6_CORE1, R6_CORE2, R6_CORE3, R6_CORE4 (under PICs).
Refer to this, part labels on PCB will be obscured:
http://www.mb6582.org/plans/MB-6582_Base_PCB_Color.pdf