It seems that some old servers have their user->idnumber declared as nullable (with some nulls within it).
In the 1.9 => 1.9.1 upgrade we changed that field from char(64) to char(255). When such change is performed, the missing NOT NULL clause is detected and enforced.
And that crashes in the old servers commented above.
Solution: Enforce not nulls are there by updating them to '' value before altering the table.