If I'm understanding you correctly, the problem that you're seeing is commonly called the peekaboo bug. It is a bug in IE that is a problem with the default style sheet that comes with MT. Do a search on MT's forum and you'll find all the info in the world about it. I never understood why MT would come with a "broken" style sheet. Yeah, it's IE that's messed up, but when most people use it, it makes MT not completely functional "right out of the box" if you will.
It's been a couple of months since I had to deal with it, but I think it is some sort of a problem with the "position: absolute" attribute. Browsing through my style sheet (a mod of the MT default) I see it in the container element, but it may be elsewhere as well. Most of the workarounds I tried broke too many things once they fixed the problem. What I found worked great was to add
line-height: 1.1;
to the element body
For some reason, explicitny giving that a value tricks IE into working right, and that is a value that is close to the default that is usually used so everything looks normal.
There are a bunch of other ways to trick IE into working right if that doesn't do the trick. Check out MT's forums.
The other possibility is to tell all of your visitors to just use mozilla....