This is not about the theme, unfortunately. It seems to me that it was likely a bug in Scintilla. I can't zero in on exactly what their fix was. But this all seemed to be be related to transition to GTK3. BTW, the nightlies look like built to GTK2, otherwise they'd comply with my current GTK3 theme.
Starting with Geany 1.34, at most, this scrolling bug does not manifest itself anymore. 1.32 is affected. If you're up for this, you could try building that version from source to see if it acts up on your end. As much as I could gather `sci_set_selection_start() / end()` is what eventually breaks the sync between scrollbar state and redraw of the vscroll slider. This scroll misbehavior just as well cold be triggered from tool-bar search field.
Geany also had a scroll-related fix [604eac9f0], but it does not look like it targets this specific issue.
Thats a general problem with distros, they may be slow to release new versions of software, especially LTS distros like 18.04.
Too bad, as I was hoping to introduce a few more "regular" users to Geany. I won't expect them to build it from sources. Hopefully, 1.36 would find its way to repos soon: [https://tracker.debian.org/pkg/geany%5D(https://tracker.debian.org/pkg/geany)