Hi Gavin,
There shouldn't be an issue with this from the IMAQdx side, so my expectation is that the registers aren't set quite right. Just to confirm, you are programming the registers once, not programming the registers in a loop, correct?
I have been looking at the manual for the camera here
http://www.isgchips.com/pdf/LW-WVGA-G-1394_Global_Shutter_Camera_Users_Guide_3_29_2005.pdf
From looking at this document, it looks like you are probably working with both the TRIGM (page 19) and IBMODE (Page 24). Is that what you have been working with?
Thanks,
Sherrie R
Applications Engineer
National Instruments