Google Analytics not tracking subpages

Hey I have Google Analytics set up for a long time now but it has not been tracking pages other than my homepage.

My site is hosted on a subdirectory like:

http://www.maindomain.com/mysite

And the tracking that I get will not go deeper than that.

I checked and the tracking code appears as it should in all the subpages but the results don’t get reported in GA.

Tracking used to work as it should before I installed WordPress, when I had a simple html site so the server did report the correct urls.

Any ideas on how to fix this?

http://wordpress.org/extend/plugins/google-analytics-for-wordpress/