OK, to clarify a bit...
ALL circuits are from the SAME 3 phase loadcenter fed from the SAME service fed from the SAME transformer. There is NO neutral involved. In fact there are no circuits with neutrals landed in this panel. ALL 208 volt 2 wire lighting circuits using 2 phases.

Two #12-3 AC (not MC) cables carry three circuits fed from separate 2 pole breakers. One circuit uses the BLACK from one AC cable and the BLACK from the second AC cable. The same is true for the REDs and the WHITEs.

At the opposite end of the run (100+feet) there is a junction box where the BLACK circuit is sent off via EMT to one string of lighting. The same for the other two colors.

The phases used are random in the loadcenter with other circuits but I am relatively certain that at least 2 and likely 3 phases are present in both AC cables.

I am wondering if anyone has SEEN a problem related to improper grouping of circuit conductors like this.