The following bugs have been reported and noted since SP2, NIM071964;NIM068933 "The Join Field tool does not match all rows even when a valid match exists. " and SP1, NIM069071;NIM066191 "The environment setting, 'Maintain fully qualified field names,' is not honored when performing an Add Join in ModelBuilder." I don't feel that it's appropriate that work around have to be applied to resolve bugs that have been around since SP1.
Regards