I hacked up a fix for this. I added an event option called onAnimationScroll - Here is the "patch" if someone wants to add it to the master
In the default options area add:
onAnimationScroll: null,
Inside the "_startAni:" function, approx line 719.
Then in side the animate = function() {
Right below the line that says "that._pos(newX, newY);"
add the following line:
if (that.options.onAnimationScroll) that.options.onAnimationScroll.call(that);
Now you can specify a call back for onAnimationScroll when you set up the scroller and then your function will be called every time an animation iterates. This works for snap, bounce and momentum animations perfectly.
Now I can ensure my overlay stays aligned with the top of the scroll area because each time a scroll pixel happens I can reposition my overlay correctly, even if the scroll happened after my mouse release during an animation.
On a side note, I had to duplicate my callback function and call it for both onScrollMove AND onAnimationScroll to cover all my bases.