Well you say in your post that you swapped the input cards, while the S&H circuits are on the output cards so it doesn't make much sense. There are 2 places i suspect the issue might be and which affect specifically that one master input or output and not other channels:
1 - At the input card some bad decoupling/filtering capacitor on the specific master input channel. This is easy to spot if you go into the !TEST menu and change the analog inputs, you should see the digital level reacting similarly. If it is steady then the problem it's not on the input side of things but rather on the output.
2 - At the output card some bad S&H capacitors (or even the opamp) on the specific master output channel. If you tap the S&H circuitry at several points with an oscilloscope you should be able to see exactly where the fault it.
It might be possibility that a bad PCB contact on the input/output cards onto the computer motherboard and that re-seating the cards just fixed it. What I usually do every time I take any card out I always clean the contacts with a bit of deoxit just has a maintenance precaution.
If the problem is still there and is on the input side of things I bet you're having the same problem but on a different fader and you just haven't noticed yet.
Cheers,
Artur