Thanks for the replies. My media is on fast external drives, I don’t think that is the problem. The media plays on the same computer in both Quicktime 7.6.6 and Final Cut Pro 7.
I am using Apple Pro Res codec but it has not behaved this way before. I think it must have something to do with the AJA driver and the version of M100 and my Mac Pro. I will try re-installing QuickTime 7.6.6. The exact same material runs fine in Media 100 on my new MacBook Pro laptop.
Charlie Atlas