What do you mean "movie like"? Do you mean black bars top and bottom?
More likely they were 14:9, there wouldn't have been any real incentive to do any other ratio. At that time it would have 4:3 or 16:9 protected for 14:9. Note that YouTube uploads are almost always not a real indication of what went out, since people can and do do stretchyvision on non-widescreen material but anyway...
Sound issues on Challenge material isn't anything new, sometimes they get mashed up when pulled. Fun House had this issue as well where the sound was unique and it looks like for some reason a portion of the audio was to be changed (presumably it was on another audio track) and so the entire thing got mashed together on the end result.
I would be surprised if the episodes were "missing" as in fell through the wiping machine. Big differences between them being physically missing, not accounted for and "not available", which covers a multitude of sins.
By movie-like, I mean that they were letterboxed in the filming style often used in movies, ie: https://en.wikipedia.org/wiki/Letterboxing_(filming)
(although the practice is used outwith movies, its where i commonly see it).
(This was observed when I watched them on TV directly and not from YouTube videos btw).
As for sound issues, while that may be true, the mere fact Challenge drew attention to an episode having sound issues implies it was that way initially when they received the tape. I can't really comment on other sound issues since I rarely saw such things myself in the past
As for missing episodes (and note this is just my speculative opinion, not a statement of fact), I can only go on what was rebroadcast by Challenge, which didn't include a few episodes. At the time (I can't find the comment in where they said this, it may have been on their Facebook group), they stated some episodes were simply not included in what they were given for S1-S4 and since they'd already indicated this batch was already assumed "lost forever", the assumption is the unincluded episodes are still lost / unable to be found.
We only know that certain contestants played on a 1998 Christmas special because they are mentioned by Chris in a book of "magic moments and more" where he talked about their gameplay, but thats all that is known: no footage of it apparently exists.
You could be correct though: they might not be "physically missing", but since no one seems to be able to find them (and given the effort Challenge went through just to get what they did of S1-S4), its highly likely they're no longer in existence. You never know though.... maybe they'll turn up somewhere.
My thoughts are that I don't believe they're not being broadcast because of a rights issue: if that were the case, they wouldn't have been likely to get broadcast rights for any of it. Having said that, I wouldn't be surprised if it was a rights issue, but I've never really heard of random episodes being blocked from broadcast because of a rights issue personally: if a whole series can be broadcast, why would one off episodes not be?