Hi Dan,
Thanks for the reply. When trying to use the connect terminals i just tried connecting the PXI10 to the onboard clock in the hope that this would configure it to use the PXI10 signal to synchronise the onboard clocks via the PLL. Doing this didn't throw any errors as i recall, it just gave me a reading of infinity as it couldn't measure the signal.
I have actually just managed to successfully do what i wanted thanks to help from Rob at NI tech support UK. There is a DAQmx timing property node which allows you to choose a reference clock source. By using the PXI_Clk10 signal this makes the DAQ synchronise its reference clocks to this signal. I have included an image of the code i used to achieve this to take period measurements.


Here is a very useful link which Rob sent me which may be of help to anyone else with similar problems
http://zone.ni.com/devzone/cda/tut/p/id/3615
Best regards,
Dan.