Aha !
I've grabbed a couple of screen shots of my HUD.
In the situations where the synced layer doesn't run, it shows that it is 1 frame behind the layer it is syncing to. (both movie files are 125 frames, 720x 576 nd were encoded using a Blackmagic DeckLink DV codec)
When it plays fine, it shows that it is on exactly the same frame.
I'll post the images once I can get them across to this windoze box.
Does this explain anything ?
Cheers
Richard