It looks like you've narrowed it down enough now.

In both cases after clicking checkbox to activate the plugin a folder is successfully created, and then Geany crashes.

The empty folders (on windows 7) are:
C:\Users[username]\AppData\Roaming\geany\plugins\Geany_Numbered_Bookmarks
C:\Users[username]\AppData\Roaming\geany\plugins\Geany_Macros


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