Hi,
I had an issue similar to yours a while ago. I enabled theming on the content pages. I added the App_Themes folder in Solution Explorer and added a blank style sheet in the folder. I then copied the /*xp theme*/ part out of the Tabs.css file in the AjaxControlToolkit\Tabs folder. I messed around with some of the items (I forget which ones specifically, sorry) to get the space to go away.
Content Page
<%@ Page Language="VB" AutoEventWireup="false" CodeFile="SiteSearch.aspx.vb" Inherits="SiteSearch" MasterPageFile="~/Main.master" EnableTheming="true"
StylesheetTheme="MainTheme" Theme="MainTheme"%>
Tab Control (added CssClass)<cc1:TabContainer ID="tcMain" runat="server" CssClass="tabBackground" Height="1200px" Width="950px" style="margin: 0px auto">
Style Sheet (this is my edited code, the code from Tabs.css is a little different)
.tabBackground
.ajax__tab_body {font-family:verdana,tahoma,helvetica;font-size:10pt;border:1px solid #999999;border-top:0;padding:8px;background-color:#ffffcc;}
.ajax__tab_header {font-family:verdana,tahoma,helvetica;font-size:11px;background:url(Images/tab-line.gif) repeat-x bottom;background-color: White;}
.ajax__tab_outer {background:url(Images/tab-right.gif) no-repeat right;height:21px;}
.ajax__tab_inner {padding-left:3px;background:url(Images/tab-left.gif) no-repeat;}
.ajax__tab_tab {height:13px;padding:4px;margin:0;background:url(Images/tab.gif) repeat-x;}
.ajax__tab_hover .ajax__tab_outer {background:url(Images/tab-hover-right.gif) no-repeat right;}
.ajax__tab_hover .ajax__tab_inner {background:url(Images/tab-hover-left.gif) no-repeat;}
.ajax__tab_hover .ajax__tab_tab {background:url(Images/tab-hover.gif) repeat-x;}
.ajax__tab_active .ajax__tab_outer {background:url(Images/tab-active-right.gif) no-repeat right;}
.ajax__tab_active .ajax__tab_inner {background:url(Images/tab-active-left.gif) no-repeat;}
.ajax__tab_active .ajax__tab_tab {margin:0;background:url(Images/tab-active.gif) repeat-x;}