There seems to be a bug in
com.webobjects.eoaccess.EOSchemaSynchronization and since it has been
deprecated, I made a workaround and some minor changes to the column
creation method. I am not sure if this bug only surfaces when adding
columns to an existing table, but it surely happens when I try to use
migrations and add a column after a table has been created. It's been
tested only with MySQL.

Within EOSchemaSynchronization the "add" SQL reserved word is replaced
by the string "null", generating a wrong SQL expression (at least in
MySQL) with something like "alter table my_table null add my_column
somedatatype" instead of "alter table my_table add my_column
somedatatype".
			
BTW, both the deprecated com.webobjects.eoaccess.EOSchemaSynchronization
and com.webobjects.eoaccess.synchronization.EOSchemaSynchronization have
the reported bug.