cross chassis pxi triggering of FlexRio with NI-Sync

[pulsed_power]

I am sending a trigger pulse to cards in two chassis:

1) PXI-1042Q with PXI-6653 (sync card "Sync") and PXI-6133 and PXI-6602

2) PXIe-1082 with PXIe-6672 (sync card "Sync1") and PXIe-6962 FlexRios.

I developed the setup based on a previous NI forum post, where you can also see my NI-Max setup (Sync0 has been renamed Sync1): http://forums.ni.com/t5/PXI/trigger-multi-chassis/m-p/3169983/highlight/true#M15036

I have connected PFI 0 of Sync to PFI1 of Sync and PFI2 of Sync to PFI0 of Sync1 with coax cables. With NI-sync I connect PFI0 and PFI2 of Sync to a global software trigger and then PF1 of Sync to the PXI_star lines of each of the cards in the PXI chassis and the PFI0 of Sync1 to each PXI_star line of the FlexRios in the PXIe chassis. 

In the FPGA code, after initializing the FPGA and the FPGA adapter I have a 50MHz timed loop look at the PXI_Star line. The PXI_Star line triggers a counter, once the counter reaches a threshold a stream vi is triggered which controls my data acquisition. However, I found that the timing on the PXIe chassis seems to differ greatly from the PXI chassis. Also if I replace the PXI-Star line with PXI_trig in the FPGA code the triggering still occurs. It does not occur if I hardcode a "False" instead of the PXI_Star line. I think  for some reason there is a pulse on the PXI Star lines before the NI-Sync initiated trigger. Does anyone have an idea what is going on?  

I am sorry that I currently only have screen shots. I am working on separating a small self-contained test case form the larger code.