For someone else struggling with this. Easiest solution is to keep the scroll location of the entire window
var xPos, yPos;
Sys.WebForms.PageRequestManager.getInstance().add_endRequest(function (evt, args) {
window.scrollTo(xPos , yPos);
});
Sys.WebForms.PageRequestManager.getInstance().add_beginRequest(function (evt, args) {
xPos = $(window).scrollLeft();
yPos = $(window).scrollTop();
});
Ad both begin and end request. On begin request get the windows scroll position using Jquery. On end request just scroll to that location.