Not sure whether it is related so just a guess:
did you try 1.29 only from the nightly builds?
They are cross-compiled with a very old gcc while the release tarballs are built natively with a recent toolchain. I don't really think this relevant here but I can't exclude it.

I hope to find some time on the weekend to test this on Windows.

Furthermore, I'm wondering about the warnings you posted, even though they are really unrelated:
16:25:55: Gtk WARNING : Error loading theme icon 'geany-save-all' for stock: Unrecognized image file format


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