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OK, now I'm a bit stumped,
I went through and re-did the code on it, still not 100% xhtml compliant, but really close to it. After I corrected anything I deemed as a potential cause of this problem, I still have the problem. It only does this with certain modules, the homepage works fine, the forum module page works fine, and some of the others work fine. Its the downloads, news, profile, and some of the other ones that seem not to work.
I have it at a set width (the main table) instead of using the percentages in the CSS. When I click on these pages, it first acts like it is going to boot up fine, then it seems as if it reads something in the code somewhere to make it break out of alignment again. I'm still sifting through code trying to find an answer, but anyone with any knowledge of what could be the problem or what could be the answer, please help.
Thanks in advance.