O.K.,
The problem is synchronisation.
First of all, I would not let individual subvi-parts of your main application save data.
Instead, I would copy the data to a memory-vi that holds the data collected from the analog and digital boards.
From another part of the program I would call this memory vi and save it's content to file.
I'm not familiar with the PCI 6602 board but is it not possible to synchronise it's measurements (measuring frequency is basically counting a number of pulses during a defined time) with the MIO board analog inputs acquisition time?
It mght be an idea to measure the frequency faster, say 10 times as often as the analog acquisition (all samples). Temporarily save the results to the memory vi.
The last frequency result in memo
ry is the last you measured so you could reconstruct a given frequency at a given moment in recent history.
This is all very non-real time, but at least gives you control over the measurements.
If this fails you could think of building extra electronics (or better, using the division options of your counter board). Take an extra analog input channel and connect this to a digital output of he counter-card. Connect the counter input to the frequency-signal.
Postprocessing the data saved to disk (and recalculating the original frequency) gives you the result you want.