It turned out that the 3c16 wires were indeed switched at the RF module downstrairs (near the bpm can).
Pete Francis and I went down to the BSY to check the bpm and do a signal test (if required) to see why we were getting Y+ and Y- mixed up. We found the RF module that collect the 4 signals (X+,X-,Y+ and Y-) and turn them in to two signals for X and Y had everything connected the wrong way and the module was lying there as if someone left it in a hurry. Pete said he had no idea who would have done that.
The signals were connected in the following way
from bpm can RF input RF output Y+ -----------> X- Y Y- -----------> X+ X+ -----------> Y- X X- -----------> Y+
So Xs were going to X and Ys were going to Y but they were all swapped. We saw with our data Y must be flipped. But we didn't see X was flipped. Thats something else to investigate. But I think since now we know which signal was going where, by fixing the channel maps we can get the correct data for 3c16 in the next replay.
We rearranged the wiring of 3c16 somewhere in the middle of Run 15656 (pedestal run). So from now onwards 3c16 data should appear with correct signs.
We also checked 3c12 just to make sure someone didn't mess up its wires too. All was inorder (phew!)