Thanks David and Graeme,
I had dropped the clip in but hadn’t included it in my process above.
As Graeme mentioned he’s helped me out via email and the problem is solved. I missed a setting which I should have changed. The end result looked lovely.
Here’s Graeme’s tips, if anyone’s interested…
Things to check:
1) that the NTSC sequence really is NTSC – that it’s 29.97fps
2) that you drop the same PAL clip into the source well as you dropped on the timeline and they have the same in point.
3) Filter is set to PAL to NTSC. Nesting should be off, rest of settings are probably ok.
4) Don’t export direct to compressor from FCP. Export a movie out first by File -> Export -> Quicktime Movie, keep current settings, make self contained.