Almost certainly one of two things is going on here...
1: Your series link is set to either "everything" or "new and reruns", the box picks up the BBC Scotland shows, doesn't see them in your 28day history so records them again. As per design.
2: Your series link is set to "new only", and BBC Scotland is showing these as subtle re-edits therefore a new "first aired date" because these are technically, new shows.
I suspect with Eggheads option "1" is more likely, but C4 (with house programs) and BBC Scotland more recently, have plenty of form with option "2"
As regards your concern over losing other BBC2 programs, no that won't happen. There's another thread recently where someone's complaining about their box recording duplicate programs because of an unrelated scenario - but the point being that TiVo is designed to "record if in doubt" - if the same show with the same first-aired-date goes out on BBC Scotland first, then your box will record that first and then treat BBC2 as a repeat. If the programs have different OAD, then both shows will be recorded.
I hope this makes sense.