I am a little confused. Pressing load address transfers the switch register into the MA. I don't think pressing load address will cause the CPU to generate a TP4 so your board will not latch the bus data. Pressing examine should read memory into the MB and then increment the MA. TP4 is a good place to latch the address for the next memory cycle although the memory boards do not latch this as it is supposed to be stable.
Your board latches the data on EMA0 through EMA2 and MA0 through MA11 on TP4. The front panel circuitry does not latch the data, it shows the live omnibus. In the case of the lamp version of the front panel the lines are buffered with a DEC380A which is a quad 2 input NOR gate where one of the inputs of each gate is grounded. This makes it an inverter. Presumably, they use this part because of the way it loads the omnibus. The output of that goes into an open collector inverter, a SN7416 which has 15V capable outputs. These are the lamp drivers. In the case of the LED front panel there is a single part that buffers the bus to the LED. This buffer is a DEC 7417 which looks like a SN7417 which is an open collector buffer with high voltage (15V) outputs. In other words, the front panel for the EMA and the MA lines is what is on the omnibus. When you use TP4 to latch the address you are not looking at the same thing as the front panel.
All this is to resolve an issue with the lower 6 bits of the MA not displaying correctly on the front panel. The front panel as far as the address lines goes is extremely simple. It echos what is on the omnibus. The first question is if the issue is in the front panel, the Major Registers board, or some other card in the machine. Any board that connects to the MA lines on the omnibus are suspect. This means any data break controller or memory board could cause issues. Also the bus terminator board touches those lines. Remove anything you can for the purposes of testing. If you have a disk or dectape controller in the machine that do data break transfers remove them. If you have more than 4k of memory remove those boards as well. The boot boards work by toggling data into memory, they don't directly touch the address lines but you don't need it for this so pull it. You don't need any peripherals at this point so remove those. You may find that pulling all the boards you don't need causes your problem to go away.
What do you see when you do a load address of 0000? Do you get all zeros?
What do you see when you do a load address of 7777? Do you get all ones?
If those work then try the patterns 0001, 0002, 0004, 0010, 0020, 0040, 0100, 0200, 0400, 1000, 2000, 4000.
And finally invert those patterns and walk a zero through the MA with 7776, 7775, 7773, 7767, 7757, 7737, 7677, 7577, 7377, 6777, 5777, 3777
If all those work the problem is probably not the front panel or the circuitry in the MA register.