You could try running Geany from the command line with the `-p`/`--no-plugins` option. It's possible that whatever debugger plugin you have loaded is not designed to fit in the message window area when it's on the right like you have it. If it doesn't happen when no plugins are loaded, try and run it normally again but change the preference to put the message window back in the bottom to see if that's what's going on.
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