If you go into your mail/htm/order_data.tpl template under 'edit templates' you can change the background colors. I copied the first part of mine (see below):
{* $Id: order_data.tpl,v 1.18.2.7 2006/02/28 11:40:26 max Exp $ *}
<TABLE cellSpacing="0" cellPadding="0" width="100%" border="0">
<TR>
<TD align="center"><FONT style="FONT-SIZE: 14px; FONT-WEIGHT: bold;">{$lng.lbl_products_ordered}</FONT></TD>
</TR>
</TABLE>
<TABLE cellSpacing="0" cellPadding="3" width="100%" border="1">
<TR>
<TH width="60" bgColor="#8B4513">{$lng.lbl_sku}</TH>
<TH bgColor="#8B4513">{$lng.lbl_product}</TH>
{if $order.extra.tax_info.display_cart_products_tax_ra tes eq "Y"}
<TH nowrap width="100" bgColor="#8B4513">{if $order.extra.tax_info.product_tax_name ne ""}{$order.extra.tax_info.product_tax_name}{else}{ $lng.lbl_tax}{/if}</TH>
{/if}
<TH nowrap width="100" bgColor="#8B4513" align="center">{$lng.lbl_item_price}</TH>
<TH width="60" bgColor="#8B4513">{$lng.lbl_quantity}</TH>
<TH width="60" bgColor="#8B4513">{$lng.lbl_total}<BR><IMG height="1" src="{$ImagesDir}/spacer.gif" width="50" border="0"></TH>
</TR>
I changed the bgColor="cccccc" to the color I wanted, bgColor="#8B4513"
You can try changing them one at a time until you see which ones affect the table cells you need to change.