Hi jstarustka,
Both your Tx and Rx seems fine and even more, when you have it working on a PFI line and not a RSTI (or PXI_Trig) line it might be due to other problems. Have you reserved the trigger lines if you have a multisegment chassis (more than 8 slots)? You have a great knowledge base here:
Routing PXI Trigger Lines Across the Buses of Multisegment PXI ChassisThis should work unless there might be a problem with the RTSI line you are using, make sure you try a couple of them. Finally, just to confirm, I would use two shipped examples to make sure this is not the code:
For the acquisition side use the shipped example called "niScope EX Configured Acquisition.vi"
For the generation side use the shipped example called "niFgen_Arb_Waveform_Marker_Example.vi"
Hope this helps,
Gerardo O.
RF SW Engineering R&D
National Instruments