Hi Zappamania,
Yes that may be case with you, in that case i would suggest you to have a look at your reqrite rules again. Thoush plugin would have been showing an error to corrent rewrite rules with suggestions but you can them again.
I am using nginx and php5-fpm and i am developing a small plugin for maintenance mode and other settings. you can have a look at the source at
https://github.com/baseapp/wpoven-manager
Thank you