Using Timed Loops

I am trying to use a timed loop in my application. The only timing source available is the 1Khz clock on the CPU. I am using a PXI-8176 CPU in a PXI-1045 Chassis. I have found that the timed loop using the 1 kHz clock is not very accurate. When comparing the loop time versus a reference clock it lags by approximately 6 seconds in a 12 hour period.
Is there a way to use the 10 Mhz reference clock available on the PXI bus?
I have also tried using the counter on a PXI-6031E card but have not had much success.

I am trying to configure the timed loop to utilize the counter on a DAQ Card in lieu of the 1Khz clock on the CPU. I have included a vi demonstrating how I plan to implement this strategy.
I have also found that if a timed loop configured to process missed iterations is stopped and placed in an idle case, it will continue to count iterations based on its period and when made active again will process the missed iterations. Is this normal?
Attachments:
DAQmx Config for Timed Loop.vi ‏94 KB

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