This post includes the solution to the original question.
It could also have to do with monitors. I know it looks awful here and I have had reports from folks in the forum that they think it unsightly as well. Also, in IE 7 there can be other problems with filters and stacking, in that the otherwise logical stacking order of elements no longer applies and sometimes cannot be brought back (depending on the design) no matter what one does. This can result in the loss of link functionality. Both of these bugs will hopefully be addressed sooner or later by MS, or they will issue a "it's a feature, not a bug" statement on it at some point.
Originally Posted by Twey
In any case, I have figured out how to enable the transitions in this script for IE 7. Find this line near the top of main.js and add the red part:
var cssFilters = ((ua.indexOf("MSIE 5.5")>=0||ua.indexOf("MSIE 6")>=0||ua.indexOf("MSIE 7")>=0)&&ua.indexOf("Opera")<0)? 1:0