Same here!!
It seems like 2004 updating installer does not care removing old databases.
1.
svchost (5380,D,12) SRUJet: The database format feature version 9080 (0x2378) could not be used due to the current database format 1568.20.0, controlled by the parameter 0x410022D8 (8920 | JET_efvAllowHigherPersistedFormat).
2.
DllHost (13392,D,12) Microsoft.Windows.Search_cw5n1h2txyewy_NOEDP_LEGACY_IDB: The database format feature version 9080 (0x2378) could not be used due to the current database format 1568.20.0, controlled by the parameter 0x410022D8 (8920 | JET_efvAllowHigherPersistedFormat).
3.
Catalog Database (5356,D,12) Catalog Database: The database format feature version 9080 (0x2378) could not be used due to the current database format 1568.20.0, controlled by the parameter 0x410022D8 (8920 | JET_efvAllowHigherPersistedFormat).
4.
Video.UI (13944,D,2) {683991B8-B0DA-4553-854D-58E57BDF4A14}: The database format feature version 9180 (0x23dc) could not be used due to the current database format 1568.20.0, controlled by the parameter 0x410022D8 (8920 | JET_efvAllowHigherPersistedFormat).
5.
SearchIndexer (8860,D,22) Windows: The database format feature version 9120 (0x23a0) could not be used due to the current database format 1568.20.0, controlled by the parameter 0x410022D8 (8920 | JET_efvAllowHigherPersistedFormat).
I've been having the same experience since updating 2004 update.