Other moms here seem to have more knowledge about this, but I hope my 2 cents still helps. I went on maternity leave twice while working. Both times, our EA stayed on top of me making sure that I had all the necessary paperwork. FMLA rules are extremely complicated, and there should be someone in your company who specializes in all that because your average employee simply can't be expected to decifer all of that for themselves.
I know that when I returned to work each time, I didn't have a release "in hand." All I had to do with each of my returns was get my doctor write a note stating that I was released to return to work, and the notes listed the date that I came back in each instance. That way, the company didn't get in trouble with FMLA rules, and I was covered for my return.
I don't see any reason why if your medical release statement gives the date you first worked after you came back as the date you're released by your doctor that HR can't give you a paycheck for the hours you've worked. I think someone in your company is very confused as to what the FMLA process is, and you need to find someone who knows the rules better.
Hope this helps. Good luck!