I really hate the for-profit servicers as well. "Obtuse" is a polite term for them. I really miss when my loan was serviced directly by the Department of Education.
To deal with this kind of issue (I had this with Verizon), I encode my payment amount so I can know what's paid and when. For example, let's say the actual amount due is $253.12. I'll put the month as the last dollars and the cents for the day. So making that payment on June 4th, I'd actually pay $256.04. A payment on July 3rd would be $257.03. So even if they don't post it to my account for 2 months, I know which payment it was.
Next, use your bank/credit-union's bill pay to send payments so you have an audit-trail. NEVER let them draft from your account - it's just not worth the
Lastly, if they're servicing federal loans and still jerking you around, write to your senators and congresspeople. They have staff who are good at helping un-f*ck bureaucratic organizations.