@Paloth - A little more info on how you went about exporting might help in solving the problem. 

Did you create all the endomorphs before doing any freezing? Create Part Names like "head, neck, chest" etc ahead of exporting? Just some more details of exactly what process you took would maybe help pinpoint the cause.

  Not sure what you're getting at when you say "freeze with the morph at it's most extreme??" 
If you freeze the subpatches while the endo morph is in base mode, you should still be able to click through all the morphs you made and export them one by one since all the endomorphs would freeze right along with the base.

Could you elaborate on what exactly you did a bit more please?

Hey! His nose is dry! ... Someone should lick it,  just in case. - Diego