IE thrashes, flashes and basically sucks on scroll reflow, layout, paints (see autoScroll hack below).
It can be eliminated by putting the autoscroll() after the slider.css('left',ptX);
But then the minScroll is out-of-sync by 5px and basically wrong, wrong, wrong.
January, 2016: MS announced the death of IE below version 11. P.S. Fix IE11 while you're at it.

Timeline
States
Notes
Slider 1
track 2
Slider 3
track 4
track 5
track 6
track 7
track 8
last row to pad for scrollbar below

IE autoScroll hack: I inserted $('#viewport').css('transition','none') just before and after the scrollLeft() calls.
The CSS has no transitions at all. It still jumps a bit but not as bad without it.