Make sure that you are re-enabling the breakpoints on your Motion board, this will ensure that you are not loosing breakpoint pulses on your RTSI bus.
In order to troubleshoot this you will need to check if the breakpoints are generating the exact number of pulses you are expecting, or if it is the DAQ board the one who is loosing pulses. There are some examples to count pulses shipped with LabVIEW, please use one of them to count the pulses from RTSI, I think is called 'Count Edges (DAQ-STC).vi'. If then you see that you are getting the right number of breakpoint pulses you can be sure the Motion board is working properly and focus on the DAQ board.
Good luck!
Nestor.
Nestor