If you are upgrading from ACE2004 to ACE2006, there is a utility to migrate all of your ACE2004 DAT files into the ACE2005 MDB file. Go to PROJECTS>EXTRAS>PLC DAT File to MDB Conversion. I had dozens of custom DAT files that came into the MDB format OK. You can also merge the parts database catalogs in the same place.
I don't recall for certain, but it seems to me that there are issues with ACE2006 and ACE2007 being install along side of ACE2004. If you un-install and re-install ACE2006 after un-installing ACE2004, do not reinstall ACE2004. Perhaps someone else can shed more light on this.