A few things you could try:

1. Try running Geany from the command line like `geany -v` and then changing 
the theme and exiting Geany as you normally do. Take note of the messages 
printed to the terminal and paste them here.

2. Try setting the theme and closing Geany using `File->Quit`, just in case the 
window manager is doing something weird and killing Geany or making it crash.

3. Try running Geany from the command line, specifying a different 
configuration directory, in case there is something wonky with your default 
one, like this `geany -v /tmp/geany-test-config`. Change the theme and exit 
normally and re-open to see if the setting was saved.

4. With no instances of Geany running, make a copy of the file 
`~/.config/geany/geany.conf` to somewhere else, open Geany, change the theme, 
and exit normally. Make another copy of that same file, and compare them 
manually, using diff, or your favourite compare tool.

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