The Domain Catalog on your Domain Search server will replicate with all of the Database Catalogs in the domain. If there are errors in those Database Catalogs, such as databases that no longer exist, the Domain Catalog will contain these databases as well, and the Domain Indexer process will needlessly check their properties.
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To ensure that your Database Catalogs are clean, consider deleting them and running the Catalog task to recreate them. If you have upgraded a server from R4 to R5, it is possible that some deleted databases are still listed in the Catalog, since R4 did not do a very good job of cleaning up the Database Catalog.