The lock that now appears in the upper right hand corner of the make-up category has a glitch. By default, a brand new sim willl generally have the lock appear "closed" meaning that the make-up SHOULD apply to every clothing category. However, it doesn't.
To truly "lock" the make-up on a newly created sim, unlock the lock and relock it. Now the make-up should be set for all outfits, any changes you make after this point should stick to all outfits.