On Windows, having multiple installations of Geany is not really supported. If I remember correctly, the Geany installer writes the installation directory (and so the path to the plugins location) into the registry. The Geany-Plugins installer reads this registry key to set the installation directory. I don't know how well it works if you overrule this logic and have multiple installations in parallel. I never tested this.
So, I would suggest to uninstall all of your Geany installations and install 2.0 afterwards. Then plugins should work. Note that copying plugin files from an old installation to a new one won't work on Windows, there are most probably never compabitle.
One more note, please be aware that we changed Geany's configuration file behavior in 2.0, many session related information (also the list of loaded plugins) has been split into a new configuration file `session.conf` but Geany 1.38 doesn't know this and tries to read the information still from `geany.conf`. And so weird things might happen when you mix Geany 1.38 and 2.0 with the same configuration directory.