I think I may have a similar problem. I have a table that I can see in ArcCatalog but am unable to delete as it keeps saying there is a missing DBMS table. When I view the geodatabase in SQL Server Management Studio, the only reference to the table I can see is in the sde.sde_layers table. I do not see it listed in the sde.table_registry, sde.column_registry or sde.gdb_objectclasses tables. Also there is no A, D, F, I, or S table that refers to the layer ID from the sde_layers table. Any idea of how to remove? Would removing it through SSMS work since it isn't referenced anywhere else?
ArcSDE 9.3.1
Windows Server 2003
Microsoft SQL Server 2008 R2
Thanks,
Chris