I always sit my classes boy girl where possible (some groups don't have balanced numbers) but I say that if I can completely trust a class to work and behave I will allow them to sit where they like. Only one class in the last 6 years has managed this (slightly surprisingly a bottom set!) You are probably having difficulties because you are trying to do the changes mid-year. That said, it is now a test of wills between you and the class. You need to punish any student who does not co-operate (even if they are nice ones) and continue to do so until they sit were they are told.