Well as the menu system is not an independant table, of course it's affected.
I agree with Paul, in that I think it's easier to do that sort of layout with frames.
However if you want a frameless layout, one method you could try would be having a master table inside which are nested (as single columns) subtables for the menu and content) see below. Been over a year since last wrote HTML, forgive me if i'm rusty. Caveat Emptor etc.
Code:
<!-- master table -->
<table>
<TR>
<!-- Column 1, Menu -->
<TD>
<table>
<!-- Your menu TR,TD stuff goes here -->
</table>
</TD>
<!-- Column 2, Content -->
<TD>
<table>
<!-- Your content TR,TD stuff goes here -->
</table>
</TD>
</TR>
<!-- End main Table -->
</table>
If you want other methods, eg all CSS, then PM me or grab them from
here (one of my pages)