Without going into too much detail, the registry of deeds is an old system that is slowly being replaced by the land registry. It sounds like the title to your property was originally registered with the registry of deeds but has since been registered with the land registry, which is the case for a lot of properties since it is now compulsory to register in the land registry (I think this now applies to all counties). As a result, it wouldn't be uncommon for a property to appear on searches in both the registry of deeds and the land registry.
But you should get a solicitor carry out searches in any case just to be sure that there are no issues with the title.