I can reproduce this also on Arch Linux with Geany 1.38. Steps to reproduce:

1. Close Geany with the Message Window open.
2. Open a file in Geany that is long enough to need a scrollbar.
3. Use Alt+V,W to hide the Message Window.
4. Scroll up and down in the file using the mouse scroll wheel.

The text view scrolls, but the scrollbar does not update.
Clicking in the text view once and then scroll some more, causes the scrollbar to start updating.

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