Heyya Robin:
Yeah – I have a minorly similar situation. I record a lot of video game footage via Hauppauge HD PVR to EyeTV software and export from there in a native (not transcoded) H.264 format. I was ‘so looking forward’ to FCPX since it was supposed to save me a massive amount of transcoding in compressor and save me lots of disc space by working with H.264 ‘natively’.
Unfortunately – i get the same image corruptions every 2 seconds and green/black blank frames periodically. Just goes to show that one H.264 is not like the other.
I will have to try it again after the OS X update that came out today to see if that fixed it.
Here is hoping that it “magically” works soon.