You should first try locking both instruments to the PXI backplane 10 MHz reference clock and see if this solves the problem. You can lock the PXI-5620 to the PXI backplane with the following NI-Scope function call:
niScope_ConfigureClock (scopeHandle, NISCOPE_VAL_EXTERNAL, NISCOPE_VAL_NO_SOURCE, NISCOPE_VAL_NO_SOURCE, NISCOPE_VAL_FALSE)
'scopeHandle' will be the variable containing the NI-Scope instrument handle created by the niScope_init() routine.
You can lock the PXI-5411 to the PXI backplane 10 MHz reference clock with the following function calls:
niFgen_ConfigureRefClockSource (arbHandle, NIFGEN_VAL_PXI_CLK10)
niFgen_ConfigureRefClockFrequency (arbHandle, 10E6)
'arbHandle' will be the variable containing the NI-FGEN instrument handle cr
eated by the niFgen_init() routine.