I use mod rewrite to make my website's forums for search engine friendly. However on pages where the user has been sent there by mod rewrite cookies seem as though they cannot be accessed via php. Is there any way to get around this?

What?

How are you rewriting the URL's? If you're making it seem as if it's on a different domain/subdomain etc then you might have that problem. What forum software are you running anyway?

There should be some config value where you set the path for you cookie (usually simply '/' will do). This is the path that the cookie will work under, so if you're cookie path is '/forums' and your mod_rewrite is making the URL something like '/showthread' etc, then that's why. Changing your cookie path to '/' should solve that.

or set them in a lower level directory....