It was found that unlink was failing for MRT tables when using prefixes. Error 4131 (CTDBRET_VTABLEEXIST) was returned when running the following command:
ctutil -sqlize .. -prefix=XX_
This was due to logic that was unnecessarily changing MRT table names when the names were extracted from the dictionaries. The logic has been changed so that the MRT table names are not altered during unlink when the table names are extracted from the dictionaries.