It is definitely a skin issue and the solution will be found in CSS. I don't currently worry about IE 6 so some of the skins we ship may not work well with IE 6 whereas some of the older skins like jsavard-mojo probably work ok still in IE 6.
To solve it you will want to override things in the IESpecific.css file rather than editing the main CSS so that your changes don't mess things up in other browsers. So you must figure out what it is in the main CSS thsat causes the problems in IE 6 then override those things in IESpecific.css which will only affect IE 6.
Hope that helps,