This seems to be fixed in 4.0, which were advertised on the Scintilla mailinglist earlier today.
From the changelist: * On GTK+ fix drawing problems including incorrect scrollbar redrawing and flickering of text. Bug #1876. I have installed it on my unstable virtual machine, and the problems as described in this bug report I had earlier have gone away. -- Andreas Rönnquist gus...@debian.org