I was having problems similiar to other posts using Parse_RDF.pl and DMOZ to add Categories and Links to an existing database and finding links scattered all over the database.
The problem occurs because Parse_RDF does not get the highkey value for Categories (High ID) when it calls mysql for it. This could be a perl problem or mysql level problem (something for pugdog or Alex to look at). What it does is try to add the new Categories from DMOZ starting at Category ID 1. It fails if the table row exists but adds the Links with that Cat ID. If there is an empty row (deleted Category) it adds that ID with the Links having that ID. The end result is an unpredictalbe mess with misplaced links and orphaned categories.
The quick and easy fix is determine your highkey (high Category ID)using the admin panels or Mysqlman and set it in Parse_RDF.pl when you set your subset, prefix etc. Set the Global my $CATID to the ID of the last Category in the database. Just remember to update it each time you run Parse_RDF.pl.
Using this method I have loaded over 7000 links and their categories with several runs of Parse_RDF.pl with complete success. I hope this help those out there have problems.