It seems that to apply the configuration changes you must restart notepad++. It'd be nice if it were not so but at the very least it would be great if PythonScript asked you if you want to restart notepad++ when necessary.
Yes, unfortunately that's a limitation of Notepad++ itself, there's no way to ask it to "re-request" the plugin commands, and the toolbar is not run-time modifiable (yet). Restarting automatically requires an external program, such a gpup.exe that comes with the plugin manager. The only issue is that gpup.exe is currently hard coded to start as administrator, which suits plugin manager, but not things that just want to restart. When I get round to updating Plugin Manager and gpup, that is something that will be there, so then we can restart easier.
Won't be in time for the next release of Python Script though - that's in test at the moment, so should be out very soon.