Did you tick always reload skin as well, then confirm?
I've just seen michaelmurrayuk's logos, he made them all with ters action, so they work better than mine. There was a problem that my small ones weren't lining up properly.
I'd download his and use them as the folders are also set out better like the ones that come with FM 07.
Although the Charlton badge he used isn't quite as good as the one I found, no white border and slightly worse quality. I doubt anyone would really notice apart from me though