Custom Magento Theme not working - php

I have installed the latest version of Magento 1.6.0.0-rc2 and tried to install the package and theme which I had developed on Magento 1.5.x
The package has been installed in magento/app/design/frontend/packagename
I have also entered 'packagename' in System -> Configuration -> Design -> Current Package Name.
In app/design/frontend/packagename/default/layout/page.xml I have specified for default 'All Pages':
<block type="page/html" name="root" output="toHtml" template="page/2columns-left.phtml">
Yet when I turn on template hints, I see that the main template being used is base/default/template/page/2columns-right.phtml.
I have verified that design/frontend/packagename/default/template/page/2columns-left.phtml does exist.
I have been trying everything to debug this, but I can't seem to figure out where it is getting 2columns-right.phtml from (which config file). I even tried to log the xml files loaded but they didnt show any of the custom xml files in the theme package being loaded.
Any suggestions on what could be the problem or what to try ?
Thanks.
Edit:
A couple of points.
Cache is disabled.
The new package/theme displays, I'm able to see the css/images/js. Some of the template files with template hints enabled are from packagename, but the main ones seem to be from base.

Page template is not set just in page.xml, but even in catalog.xml, catalogsearch.xml, customer.xml... I mean, almost every pages have his own layout.
The layout set in page.xml is valid only for CMS pages. All other pages have other settings that override it.
Which page are you looking at? A category page or a CMS page? Try different pages and see what happens!

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Also what's Joomla Site with gk_magazine template mean too?
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I've attempted to copy it into the Woocommerce directory I created in my theme's root directory and modify it. No dice.
I've also attempted to modify it directly in the Woocommerce plugin directory. No dice there either.
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I was able to fix this by using the suggestion here - Changes on archive-product.php doesn't work
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I'd love to know the reasoning behind this.
Switching to the twentyeleve/twentytwelve theme's and trying to override the archive-product.php file in the same fashion worked great, but they don't include a native woocommerce.php file in their root directory either. What gives?

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