For a reason beyond my skills, the application seems to be indeed using the MySQL prototypes instead of FrontBase's to create the _dbupdater table. My model surely has the FrontBase prototypes selected, but this seems not to influence the prototypes choice by ERXMigrator or ERXJDBCMigrationLock. So my solution was to create the _dbupdater table by hand and populate it with the models I use. After this intervention the migrations worked again.
But the question remains, from where does ERXMigrator take the prototypes information?
Cheers,
Angelo