This behavior, where the scrollbar thumb is displayed in a different location
from where Tk thinks it is located, was fixed when the scrollbar was rewritten
to draw it directly rather than by using HITheme.  There are many lines of
comments about this in the code.

Since your toolbar buttons have reverted to looking like they used to look a year
ago, and your scrollbars have reverted to behaving like they did a year ago, I
suspect that you are not running the version of Tk that you built from the
current core-8-6-branch tip.  Some strange things can occur with Apple's launcher
when you have multiple apps with the same bundle identifier.  Please look around
for old versions of Tk.  And please make sure to completely remove the build
directory before building Tcl and Tk.