After Upgrade Links do not work

I just upgraded to 2.5 and have a problem with the links inside the site. Prior to upgrading all the links worked. Now the links don’t work. I checked the code and it is correct but when I hover over the link there is an added goto?php added to the link. This is an example of what I see:

http://www.shoalnreef.com/go.php?http://www.shoalnreef.com/shoal-n-reef/fishing-videos/

Notice that there are now two http://s in the link. As a result I get:

404 – Not Found

Posted as not found
The post / page you are looking for, is not found on the site now.
It would have been moved / deleted. You can browse or search through the archives.

The page is there and the link is correct in the code. Do I need to tweak something to make it work correctly.