Basically ASPNET Doctype doesn't recognized 100% Table Height and WebZones will rendered as Table in the page.. As a remedy for this you need to use this doctye below to work the 100% Height.. see below demo
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<table style="width:100%; height:100%">
<tr>
<td style="width:100%; height:100%">
<asp:WebPartZone ID="WebPartZone1" runat="server" Width="100%" Height="100%">
</asp:WebPartZone>
</td>
<td style="width:100%; height:100%">
<asp:WebPartZone ID="WebPartZone2" runat="server" Width="100%" Height="100%">
</asp:WebPartZone>
</td>
</tr>
</table>
You may also read this article for more info
http://apptools.com/examples/tableheight.php
Hope that Helps!
Vinz