When this glitch is happening, is there any output on the console? (Start Geany with -v option)

Another thing would be to run Geany with GDB and see if fires off a lot of threads (GTK+ does this sometimes and it can block, I guess when they're joined). Additionally, in GDB, if you're fast enough and can interrupt it using Ctrl+c while it's stuck, the resulting backtrace would probably be useful to see what's it's doing.

A final thing to try might be to run Geany with GtkInspector and see if anything looks fishy with the signals as @elextr mentions.

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