I'm not sure that pushing extra money toward this student loan would require a phone call every month. It might simply be a matter of pushing money at the debt instead of using auto-pay.
There are basically two ways to pay extra -- either make a larger-than-necessary payment before the auto-pay date or make a top-up payment after auto-pay has gone through. The first option is easier but it requires some confidence that making the payment on your own will suspend the automatic payment. The second option is to keep track of when the auto-pay is supposed to happen and make an extra, top-up payment after it has gone through each month.
I'm not sure that calling the lender and telling them how to allocate the extra money is necessary as long as the amounts sent are less than twice the minimum payment (under the first scenario) or less than the next payment (under the second option).
I'd probably experiment instead of trying to make more phone calls demanding explanations. I'm not good at understanding what I am being told in such phone calls, or believing it, or remembering it after the call has ended. I'm the sort that trusts what my statements say instead of what I was told on the phone. Call me a chickenshit if you must, but I hate making those calls and don't like being tied to making them during business hours.
Yup, they were probably relieved that you were neither yelling nor crying. I'm sure that they get way too many of those calls. If what they told you is true, can you imagine how often they have to field a call from someone who thought that they were making three months of payments at once and is now facing delinquency or default?
Sometimes it is good to remind yourself that no matter how crappy the service that you receive seems, at least you aren't the one having to deliver it or field the consequences.