Probably the problems were caused by commenting things out rather than removing them. If you make the slightest mistake in layout.master it will fail to load, log the error in the mojoportal log and fall back to loading a failsafe master page to keep from crashing the site completely (though it can crash the design since the failsafe one doesn't have the same stuff as your custom design).
For server controls you cannot comment them out with html comment syntax.
For example this is html comment syntax, it can be used to comment out raw html
<!--
<a href="http://somesite.com">Link to Some site</a>
-->
This is comment syntax to comment out a server control:
<%--
<portal:PageMenu ID="PageMenu1" runat="server" UseTreeView="true" IsSubMenu="true"
TreeViewShowExpandCollapse="false" />
--%>
If you try to comment a server control with html comment syntax it will cause an error. Though in layout.master you can comment out raw html using the server syntax. One advatage of using the server syntax to comment out html is that it won't be rendered whereas if you comment out html with html comment syntax you can still see it viewing the source of the page.
Hope that helps,
Joe