I have developed couple of extensions and never had any problem in deploying to the production server. I did try to installation a new extension today on my production server that works on my dev machine but doesn't work on the production server. I am suppose to see a new menu option as part on this new extension and I don't see that. To test I changed the extension name in the production.ini and I got an expected error (PlugInNotFoundError). I have restarted the apache and nginx. I am running CKAN 2.1.
I did ran the following command on the production server: 
python setup.py develop
I got the message that the plugin was successfully installed.
I also included this new plugin in the production.ini file settings.
Restarted both the apache2 and nginx servers.
Still not seeing a new menu option to access the functionality provided by this newly installed extension.
Any help to sort this out be appreciated.
Thanks,
PK
Do you need to clear your browser's cache? Are there any other settings (e.g. extra_public_paths) that are different between your dev and production machines?
CKAN extension deployment not working