I am a recent graduate currently working full time for a nonprofit through a national volunteer program. I have consolidated my loans and because of my stipend income I am currently paying $0 under the IBR plan. However, I am confused because my first couple “$0 payments” are not showing up on the direct loan servicing website as payments. I wasn’t sure if there was any action required on my part for these “payments” because I was required to pay $0.
How do I prove that I made these qualified, on time “payments” while working for a nonprofit when the amount due is $0?

The regulations are clear that when payments under IBR are calculated as $0 due, then $0 counts as a payment under IBR.  As for how they are showing up on the site, that’s a huge mess for a lot of folks.  I suggest that you complain in writing, and get and file those new employment certification forms ASAP: http://askheatherjarvis.com/blog/3-new-documents-everyone-in-government-and-nonprofit-services-needs-right-n