The somewhat infamous scaler gating problem is being caused by the time difference between the clear scalers (happens on Prestart in the Left Arm) and the go signal.
My theory is that the way 2.6.1 does state transistion what happens is that all of the ROCs beside the trigger supervisor go through their state transisition, then the TS. Since the TS on the Left and Right arms aren't acting like TSs what happens is they get the prestart end prestart commands and then wait in a strange state while BBTS1 goes through it's prestart.
This means that the TS in the Arms counts for a while as the hardware inhibitor signal for the scalers only happens during start and prestart, but the strange inbetween state is when the TS goes into pause. So the scalers count during Pause.
This could be fixed by simply moving the scaler clear code to the start section of the ts_scaler_Left.crl.
I did this, the backup file can be found at ts_scaler_Left.crl.8Mar2011.
We will attempt to implement the new code after lunch,