When the current session was a CTSESSION_SQL (i.e. automatic handling of SQL system table on table create/alter and drop), ctdbAlterTable(...) removed granted permissions and synonyms from the system table. The logic has been enhanced to eliminate this problem.
A similar problem occurs in FairCom RTG when running sqlize on tables already linked into SQL. That problem has not been fixed in this modification.
Note: This modification is a Compatibility Change.