Ah! So it seems my beautiful new design was (and still is) having some trouble validating to the W3C Standards! But how could this be?! As it turns out, this Ajax Search script (which I did not write) was the cause of all the trouble. The form template was missing a fieldset tag, and I had to go through a long process to find out where the code was even located. I added the fieldset tag and then went on to modify some more code (since this also caused a bug with the script). As of right now everything should be validating to xHTML 1.1. If you catch a page (or an article) that doesn't, please inform me using that e-mail form that I haven't made yet.
I am also now having some issues validating my CSS for the page. The ajax search script strikes again! Apparently it is using the CSS3 opacity property to hide/show search results (oof!) I tried fiddling with the javascript files briefly, but made no progress. So I'll try again later and/or make a word around for it if I can't find a solution. So much trouble for such a useful neat little script!