Please note that there has been two typos in my Base Master Page file.  I have uploaded a corrected version and it is available on the Base Master Page web page on my site.

Typo 1

In the HEAD area of the master page, the SharePoint tag pulling in the Theme was before the SharePoint tag pulling in all of the CSS files.  This resulted in overriding your custom themes with the default SharePoint CSS styles which meant you canceled out any Theme you applied.  In your existing master pages, make sure the following tags are in the HEAD in this order:

<SharePoint:CssLink runat="server"/>
 <SharePoint:Theme runat="server"/>

Typo 2

I had an extra closing DIV tag in the Quick Launch area after the SharePoint:SPLinkButton tag in the View All Site Content block of code.  This can cause you grief if you are working with DIVs in your master page since it could prematurely close an opening DIV tag.

Thanks and sorry!