Samples missing when two DAQ boards synchronised

I am attempting to synchronise the input from two NI DAQ cards using the RTSI bus: an analogue PCI-6110 card (slave) and a digital PCI-DIO32HS card (master). I think I have the cards working OK together now and they appear to be taking samples in sync. However, although both cards are configured with the same size buffer the analogue card never seems to complete it's aquisition and always records 3 scans less than the digital card. Does anyone know why this happens or how to get both cards to aquire the same amount of scans.
See attached code for details. Cheers, Tim
Attachments:
Analogue and Digital Capture11.vi ‏4658 KB

I believe the 6110 has a analog input pipeline depth of three samples. This is from the NI-DAQmx help under Device Considerations -> Timing -> S Series: if the pipeline depth for a device is three, the first sample will be acquired on clock tick 1, but it will not be available for reading until clock tick 4. Following this logic, you must supply pipeline depth extra clock pulses for a finite acquisition to flush the pipeline.

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