Using the image from 
ftp://st.cs.uiuc.edu/pub/Smalltalk/Squeak/3.9/Squeak3.9a-6548.zip, when I try to 
use the scrollbar of the "Welcome to..." window or to open the "ReadMe.txt" or 
the "A Word of Caution..." windows or use their scroll bars afterwards, I get a 
notifier saying:

"PluggableTextMorph(ScrollPane)>>scrollBarValue: has been deprecated. Please use 
vScrollBarValue: or hScrollBarValue: instead."

for each movement. I can proceed or abandon and things go forward, but it's a 
bit annoying...

I won't pretend to understand all the details, but this doIt fixed the problem 
for me:

candidates := ScrollBar allInstances
          select: [:m | m slotName = 'scrollBar' & m model isKindOf: ScrollPane].
candidates
    do: [:c |
       c instVarNamed: 'slotName' put: 'vScrollBar'.
       c instVarNamed: 'setValueSelector' put: #vScrollBarValue:]

Apparently something in ScrollPane changed and these existing ScrollBar 
instances weren't updated accordingly.