I like it. One thing that I would recommend is to get rid of the big blue box on the homepage that says "Home" because you are already on the homepage of your site. There really is no point to link to your index if you are still on it.
Which text has been changed to a hyperlink? I'll look at it and tell you how to fix the problem.
Firstly, I think that you need to remove this snippet of code <center>Radio Blackout Level: <a
onclick="_gaq.push(['_trackEvent', 'Outgoing', 'www.swpc.noaa.gov', '/alerts/archive/current_month.html']);" href="http://www.swpc.noaa.gov/alerts/archive/current_month.html" target="_blank"><img
src="http://www.swpc.noaa.gov/SWN/r_past.gif" alt="Solar data"/></center>
next, make sure that you end links with </a>. If you do not add that on the other side of the <a> tag, then the link will continue to all other sub elements.
website has totally changed
Not for the better, I'm afraid. At the moment, it's just the packed/encrypted site encoding. If you're using a Zend-encoded script (either something processed with Zend Guard or built using any of several site-building software packages), it's not being recognized by the server. There could be a number of reasons for that, but the one you'd have control over is checking the byte order of the file(s). Did you develop and test locally on a Windows system?
Much better. One big problem remains, though: you're using fixed width design that's wider than a lot of users' screens are going to be — netbooks (and small "ultrabooks") as well as tablets need to scroll horizontally to see your header menu. It would be better to let the menu items float and wrap as necessary.