The location of your content directories is not significant, as long as you can access them. Yes, if one with "bad" files is still connected they will be read, unless the "good" version (if there is one) is earlier in the list of content directories. It does sound as if you have one or more morphs isntalled with a non-zero default - if you load the plain base figure and go to Edit>Preferences>Zereo>Zero Figure Shape does it change?