That little space is an annoying one built into rectangle_bottom.tpl. I usually just remove this bit of code:
Code:
{if $config.Adaptives.browser eq 'MSIE' || $config.Adaptives.browser eq ''}
<TR><TD height="100%">[img]{$ImagesDir}/spacer.gif[/img]</TD></TR>
{else}
<TR><TD>[img]{$ImagesDir}/spacer.gif[/img]</TD></TR>
{/if}
Sounds like a caching issue on your IE browser. Dump the cache and see what happens....