Perhaps the bug I reported in 6.4x's MED since the first (or second?) public beta came out that hasn't been fixed yet could be to blame? Is this what you're having difficulties with? This happens when trying to build faces that span multiple groups.

If it involves the skin edittor, there's yet another bug, of which I reported when the first public beta came out that hasn't been fixed yet, when your texture is not square (a 4:1 ratio and further nonsquare is where it's really bad). It's actually still possible, but extremely difficult.