It runs out OK to my ref monitor through the Blackmagic card, which suggests its an After Effects issue rather than hardware.
Why not? Sounds exactly like that - the BMD card is using the card's resources/ grabbing its buffers and then simply cannot handle stuff that doesn't match with the TV/ video spec chosen for the card which is kinda logical... (to me, anyway)
Sounds like hardware IO problems to me. If you can still see the comp in AE and only the external output is fouled up it's almost always a hardware or a hardware driver issue.
Thanks for the responses guys. I think I may not have explained the problem clearly, sorry. I am getting a clean feed to my PVM through the BMC, it's the preview in the After Effects canvas window which is displaying blue. As I say it's intermittent, and it displays the timeline correctly if I zoom the window up or down, or do an ROI on it. The display is connected via DVi to a quadro 4000. I've updated the Cuda drivers. Also, final cut and premiere are previewing fine, which makes me think it's AE6.