That's a really useful clue, and I think you're right — this is now looking much more like an A6 switch/input problem than an LED problem.
When RESET is held during power-up, switches A4-A7 select the baud rate. With all four switches down, the value should be 0000, which selects 9600 baud.
4800 baud corresponds to 0100 — in other words, the firmware thinks A6 is raised.
That also fits with the A6 LED being on when the machine is halted. It may simply be displaying what the Arduino believes the switch setting is.
A6 is read on Arduino Due pin D68. The switch inputs use the Due's internal pullups, so with A6 down/off I would expect D68 to measure roughly 3.3V, and with A6 raised/on it should be pulled to approximately 0V.
Could you measure D68 in both switch positions?
If it stays near 0V in both positions, I'd look closely at the A6 switch, its solder joints/traces, and the connection to D68 for a short to ground.
Also measure continuity on the A6 switch. When the switch is down, the top two pins should be connected, when it's up the bottom two pins should be connected.
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