In a Cosmos Motion simulation I have a shaft set to run at an
angular velocity interpolated from a bunch of points I input. I
mated another shaft to it using a 1:1 gear ratio but when I check
the angular velocity of the second shaft the angular velocity
magnitudes don't match.
The shafts are not touching but I don't think that should affect
the results.
Update: Our VAR responded and said he found the same bug in the software and has to forward it on as a bug. Will update as I found out more.

Update: Our VAR responded and said he found the same bug in the software and has to forward it on as a bug. Will update as I found out more.
Would it be possible to upload your input points and/or model?
Depending on the number of points, the results can vary quite significantly. But you are correct that it doesn't matter if the gears physically touch. The 1:1 ratio determines the interaciton.
Thanks,
Ian