My points were posted shortly after each stay. On my online account page, I saw a progress bar indicating % completion. I ended up completing and obtained 10K points. If you never saw that in your online account, I'd call them and mostly you may have to fax them copy of e-folio to claim points.
Sounds like you might not have registered (or MR might not have recognized it) to Megabonus before you started the program.