here is the code for the left column
<td width="20%" bgcolor="#EFEFEF">
<!-- Start left blocks loop -->
<{foreach item=block from=$xoops_lblocks}>
<table cellspacing="0" cellpadding="2">
<tr>
<td class="blockTitle"> <{$block.title}></td>
</tr>
<tr>
<td class="blockContent"><{$block.content}></td>
</tr>
</table>
<{/foreach}>
<!-- End left blocks loop -->
and for the right column w/blocks
<{if $xoops_showrblock == 1}>
<td width=20% bgcolor=#efefef align=center>
<!-- Start right blocks loop -->
<{foreach item=block from=$xoops_rblocks}>
<table cellspacing="0" cellpadding="2">
<tr>
<td class="blockTitle"> <{$block.title}></td>
</tr>
<tr>
<td class="blockContent"><{$block.content}></td>
</tr>
</table>
<br />
<{/foreach}>
<!-- End right blocks loop -->
change the bgcolor for those td settings or make your own reference in the css file for those columns.
as far as the grey spaces between the blocks on the right column, it looks like you have a break tag in the right block code which is showing the column background instead of the block background. so every time it loads a block, it throws a break tag in between each block.
delete that, and it should look like the left side.