I have had similar challenges. It works in Safari and Firefox on Mac. Not as expected in Chrome.
In Chrome, it is not possible to scroll the iFrame, unless quickly taking the scrollbar while it is visible during the page load.
My setting on the Mac is to only show scrollbars when scrolling. If OS X is set to always show scrollbars, I get two scrollbars in Chrome. There shouldn’t be any for the main document, but there is one. Chrome seems to always shows a scrollbar for every page, even if not needed. So a bit different in this case, compared to Safari. Firefox is somewhere in between.
Maybe Chrome has dropped some support here, during an update recently?
It is like 1997 again. I just love web technology…
With may tests on iOS; iPhone 6, iPad 2, latest iOS, the iFrame scrolling works. (But I get other problems on iOS with my iFrame-solution, waypoints are not triggered.)