I also have this problem. Not sure what about the esp is causing it though =/
Orphaned references in the worldspace group. Sometimes, with FO3Edit while copying cell, worldspace, and dialogue records, records and/or groups of records copy over without their parents, thus leaving them 'orphaned'. In this particular case, it was references from Fallout3.ESM which Beth had Ctrl+X'd ("deleted") in Broken Steel.ESM which UF3P removes in a stable, reliable manner. http://www.mediafire.com/download.php?jwhxz4h0tm0's a fixed version which assigns those references to their appropriate cells for the time being until Quarn releases an update.
http://i196.photobucket.com/albums/aa150/JustinCoherent/Fallout%203/OrphanedReferences.png. If you ever see this in TES4Edit or FO3Edit, delete the children, save, then reload and try again as sometimes it takes multiple attempts before intact subrecords will copy over and they're REALLY easy to miss since they're hidden as subrecords.