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