OK, more information inbound.
This line of code;
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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seems to be at the root of my issues.
If I put my Javascript in before that line, the Navigation works but the posts in the threads load incorrectly.
If I put the JS in after that line, the posts load correctly but the Navigation doesn't work correctly in the way detailed above.
Is there a DOCTYPE I can use and get what I want. Despite despising IE as the root of all of these issues I am having, the majority of my users use the afore mentioned browser. Thus and therefore, I need to get this right.