The attached patch should fix the problem with synchronization in procedure vscroll-sync. I've tested this under Unix, and should also work under Windows and Mac.
Please note that not using "sync" (or "count -update -ypixels" as work-around) is a bug, because "yview moveto" is not designed to synchronize automatically, and "yview moveto" does not work properly if the line pixel information is not up-to-date. (The line pixel information will be computed asynchonous, and command "sync" ensures that this information is complete.)
This patch is a must when using the revised text widget implementation, because this widget behaves a bit different - but still conform to documentation -, see Revised Implementation of Tk Text Widget.
Applied to https://github.com/brianwalenz/tkdiff, but not tested.
As of V4.3 this patch is no longer required.
Also be advised that while the fundamentals of this patch are correct, it only addressed a portion of the root cause (the TK 8.5 upgrade); some degree (possibly substantial) of visually misaligned scrolling will still likely be observed.