Skydriller
I don't know the actual routes that you are talking about, but I suspect that it might be a result of that old adage the 'code-share'.
If for an example you are flying on a SK flight from the UK, but using a BD flight number then an eticket is not available and you will have to have either a paper ticket or a Ticket on Departure.
BD very often offer lower fares then SK on the same aircraft, so you have the choice of either a eticket at a slightly higher fare or at the lower fare and then pay an 'excess' for the paper ticket. I'm afraid it is a Catch 22 situation.
Only when all the airlines have introduced Interline e-tickets will the problem go away.
Hope this helps