The sudden loss of inertial scroll on one of my websites has had my head scratching for literally a year.
When I ran into it again, alongside issues with scrollTop() always returning 0, and being unable to move the viewport on mobile, I stumbled across the fix: html/body must NOT have a height set to 100%.
Sadly, the sticky footer solution I use requires 100% height (and no min-height will not work). Ultimately I have ended up repeatedly using both media queries, and JS based platform detection to target styles most effectively.
There it is though: if you have issues with inertial scroll loss or scrollTop not functioning, check if you have html/body set to 100% height.