Have you resaved the clothing at any stage?

Some clothing is "super-conforming" which means that at least some of it's morphs should be automatically slaved to the morphs in the character.

If you save a character along with a conformed super-conformer to the Figures pallet, it should still work the next time the cr2 is loaded, but if you save a super-conformer to the Figures pallet by itself the super-conforming will be broken.