If my understanding of automated playout systems is correct, then all the problems are likely to be related.
My understanding is that digital "flags" are added to frames of a video dictating where the playout system should start playing (e.g. after the countdown, a frame or two before the titles start), where the playout system should pause for an advert break (and how many frames to skip when resuming), where the CA should kick in (if at all) in the titles, and where to end the programme.
It seems that when Sky moved Challenge over to their own playout facilities - these flags got screwed up. If they were able to import them from Red Bee, the process went wrong - however my guess is that they couldn't be imported over so they had to be added in manually from scratch en masse (which must have been a fun job!). Obviously when you're doing this with thousands of hours of content mistakes are bound to happen.
The problem also exists on some other programming which moved to Sky playout in January - I've noticed it on Fresh Prince of Bel-Air on Living Loves for example.
You're not far off.
There aren't 'flags' as such, but there's a database in the playout system which will have the timecodes for the start and end of each part of each media clip. The paperwork from the distribution company accompanying each tape might have had the correct durations on it, but it's more likely they'll have been generated from scratch by Sky - after all, why would Red Bee want to share such information with a company they've just lost a playout contract to?
(there are probably technical reasons why this wasn't feasible too.)
It's possible that there's something clever in an ingest system which marks the start of a long stretch of black & silence as the end of a part, but what's probably more likely is that a bored tape jockey hasn't been briefed on their job very well, and marked the out point as the last frame of vision. It's the sort of thing that a playout director ought to spot while previewing their junctions, but perhaps Sky don't do that. (If they did, you'd probably start seeing a lot more 5 second fillers to make up the time)