Have you considered refinancing to get to another lender? Depending on the current terms, it shouldn't be any more expensive; most consolidation loans are an average of your current rates - and just because their system is screwed up, your BF shouldn't have to risk his credit getting messed up if they report it to the credit bureaus the way they're reporting it to you.
Also, many of the student loan lenders give you a discount for electronic withdrawal (mine gives me 1/4% off) and a further discount for on-time payment (1/2% after 1 year, 1% after 3 years) - it's a gimme since the auto-draft is never late. I'd really suggest checking around for a better lender; even if he gets the same terms he's got now, there are usually no fees, and there'd be less headache.