As far as I can tell, it's not that they're skipping episodes, rather there's something very wrong with the meta data that the TV guide gives.
My TiVo recorded (what it said was) Haven on Friday evening, and then yesterday it recorded (what it says is) Lonely Among Us, episodes 11 and 7 respectively. I checked the recordings, and they're actually *both* The Last Outpost, which is what should have been on on Friday.
So, it does seem like they're broadcasting them in the correct order, just with the wrong details. For anyone with a Series Link (particularly on TiVo), this may well mean it catches the same episodes multiple times, and misses others, so it might be worth setting them all manually - I noticed that TiVo had already cancelled the recording for this Friday and next Monday, as it thinks both of those are Haven again.
Hope that helps people!