Ah yea, these things happen.
The board i have was an ebay sale with reported display problems.
Someone messed up the 60hz mod and pulled the 5v and signal pads from the board.
Got that fixed, then found the first port had barely enough to power the adapter and 3d controllers.
After a clean and scrub, it got worse and only worked with digital mode from then on.
Then port 2 followed same problem.
The meter was reading enough continuity to shade another problem under the first emi filter, not related.
The pad had lifted and the track was pitted badly somehow but still close enough to the pad origin to jump.
As soon as i touched it it disintegrated.... so a bare track to solder to and a bit of mask was enough to sort that.
Even the SMD/Genesis had that issue with some of the caps that had just started to fail along with a near catastrophe involving the vrm.
about 3 caps had pads that just dissolved upon contact
The board has had some attempted repairs before it got to me, there's another blob of mask covering a component(capacitor?) near the output.
No idea what that's all about, maybe a drop spill.
I popped the board in the box for a full test, both ports at full power now, system performs well.
So just waiting for those bits to switch out port 1 emi filters with 0-ohm resistors and switch the 2 jumper wires with an smd component.
I'll likely leave port 2 emi filters as is for now.
Drop a pic here of the area on your board when practical, I'm sure we can jury rig a solution.