Have you measured the resistance between wiper and CW and then CCW on the output pot in those positions? Those pots have 20% tolerance, so if you happen to have one with lower resistance and the other with higher resistance still within the tolerance range that would explain that. Even when stereo linking them you will have to adjust the outputs independently to get them to match.
Also, 1k tone is not a good test for matching with the 1176's. I've had similar issues you have doing the same thing, but when I did the same test with a stereo drum stem the knob position were much closer to being at the same positions. There is a bit of a write up on the Hairball Audio site that deals with linking 1176's. I think it's still there. If both units are working properly and sounding good with no hums or buzzes then I wouldn't put too much stock in the knob positions.
If your OCD won't let you look past this knob position discrepancy like I experience sometimes, then you can do these things to see if you can get them more closely matched:
- Turn in and out knobs all the way down and make sure the indicator line starts at the same position.
- Recalibrate them side by side
- Replace the pots with ones that are more closely matched.
Report back and let us know.
Thanks!
Paul