If the code is the same then the results will be the same, so...
Pagination is really quite complicated and depends on "honest" options to work--that is that if you say there are 3 thumbs in a row and your theme does not show three, things may not work. Simlarly, it you do not exhaust a loop Zenphoto will not know the pagination is off.
Simply put, if this works on standard themes and not on yours you have done something different.