The links on the Frontpage keep changing!!

I am having a large problem with my installaton. Having just installed a new template I am experiencing frequent changes to the URL.
The url to my installation is www.mysite.com/forums/
So, for example, if, when the links are working do I hover my mouse over the 'Latest Topic' table on the home page, the link is www.mysite.com/forums/showthread.php.... but sometimes, it randomly changes to www.mysite.com/showthread.php... after you view a few pages and return to the home page or whatever.
I can't understand as to why this is randomly occurring.
Any advice?