We checked to make sure that the TDC Calib module (the module fanning out the reference channels for BOTH the 1190 and the F1TDC) was operating correctly. It seemed alright from the scope. Run 2838 showed that we are missing about .4% of hits in the F1TDC and that all the reference channels (2) are missing when either are missing. The CAEN 1190 shows that it has the reference channels for those events.
As such we swapped one of the two reference channels that was in the 1190 with one of the reference channels in the F1TDC. We also added two more reference channels to the F1TDC beinging the total number up to 4. We see the problem in all 4, when one is missing, all four are missing, but the 1190 has both of its reference channels.
This leads us to believe that the problem is with the F1TDC (running in NORMAL resolution mode). I will follow up with the DAQ group about it tomorrow.