In a Wordpress/Buddypress installation, I am having to go through all my code and manually insert ampersands. For example, where there are links to things such as "?r=user" I am having to convert that into "?&r=user" in order for the link to do the required function. Or when it says "?_wpnonce" I am needing to change it to "?&_wpnonce".

Am I missing something? Is there an easy rewrite rule I can use for Nginx to fix this?

I am on Nginx only, not using it as a proxy to Apache.