When you say separate power sources, I'm assuming you mean different transformers... but ultimately from the same utility lines. Somewhere in the transition from utility to control power, you are creating a phase differential.dwanderson said:
You mentioned trying L1-L2, L1-L3, L2-L3. You should also try L3-L2, L3-L1, and L2-L1. This would test for inverted phasing of the control transformers, where the output creates a 120/240 situation. You may otherwise be creating two 120V legs of a 208 wye system.
If you check all six possible combinations and none of these give you a near zero potential difference, measure your voltage between lines of the different sources, e.g. A-L1 to B-L1, A-L1 to B-L2, and A-L1 to B-L3 (there are six more combinations but these three should suffice). While it is not required for the sources to be aligned phase-wise, the readings you get may explain the voltage difference between control hots. Perhaps your source transformers are connected differently, i.e. one delta-delta, the other delta-wye...? ...or you have like phasing and rotation, but the lines are shifted, i.e. where one source is ABC and the other is BCA or CAB.
The remedy may be simpler than you think...!