Basically removing that code broke the links because thats what the code was for but it was causing conflicts with the MyBB javascript, try adding this back and seeing if that fixes your navigation menu:
<link rel="stylesheet" type="text/css" href="http://www.sparkonline.net/forums/css/ddsmoothmenu.css" /><!--[if lte IE 7]><style type="text/css">html .ddsmoothmenu{height: 1%;} /*Holly Hack for IE7 and below*/</style><![endif]-->
I was actually reading
this page to see if I could take the original code and put jQuery into a mode where it wouldn't cause any interference with myBB. But your code worked. Links are back to the way they should be and the code editor and smileys are working. Thanks!
Does your menu actually need jQuery though? I couldn't find any drop down menu or anything which would require it.
No, the navigation links doesn't require drop-down menu coding...but i dunno...without that code, the navigation links break.
It's understandable that the CSS would make it break but not the Javascript (jQuery) which is what is causing the conflicts. But any way, if its all working now then don't worry about it.