EVERY link is opening in a new window. I believe this code to be the culprit:
<base target="Main">
Now, unless I am mistaken, the code shown above (taken from your document's HTML) is telling the browser to open every link in a frame called "Main". Since that frame cannot be found, the browser simply opens the link in a new window.
Not a PHP problem, but HTML (unless I misunderstood your question).
HTH