Jesse,
I remember having trouble with this before, but it's been a while. The thing that comes to mind is to do an F_ApiSimpleImportFormats() after you apply the pages, being sure to import page formats and removing overrides. Just use the formats in the document you are working on, something like:
F_ApiSimpleImportFormats(docId, docId, FF_UFF_PAGE | FF_UFF_REFPAGE | FF_UFF_REMOVE_EXCEPTIONS | FF_UFF_XREF);
I don't know for sure if that will work. Just an idea.
Russ