Deciphering Google Penalties

A poster in webmasterworld.com posted asking how to Deciphering Google Penalties, That post sounds pretty interesting so I am posting it here,

Trying to determine the type of penalties given by Google, seems to lead to a lot of differning theories, and I am finding it hard to determine who is correct: I will give the following example that I am having, my theory on what the problem is, and am interested in hearing what the SEO experts have to say.
Our market is rather niche with what I consider low to low-moderate competition. Their is only about 10 major players in our industry, with maybe a 100 or so want to-be’s, which pop up year to year and disappear.
Optimizing for the top 10, should not be to difficult, and for the past 5 years, we have ranked #1 or #2 for our popular keywords. After Florida we were still in the top 10 after disappearing for a few weeks.
For the first few years, our site was widget.ca, and then we got a widget.com domain. We got our ISP to enter an AName (or was it a CNAME alias) in the DNS entry, so the same two names pointed at the same IP address.
Google duplicate content filter, always filtered out the widget.com from the search results and always displayed the widget.ca when searching for our popular keywords.
Around mid september, after several years of this behavior, Google now chooses the widget.com instead. The site:widget.ca -something proves the .ca is gone and the widget.com shows up with the site: qualifier.
Both widget.ca and widget.com have a PR of 5 (4 after the last PR update in late september). However the only way to get my widget.com listing to appear in the top 10 is to put the exact worlds of our title text, as the search entry.
The widget.ca site had four times the links of the widget.com, however shouldn’t the links be combined when determining PR, when you have two URLs that point to the same IP address.
If the PR was not combined, I should still show up in the first few pages, as the keywords are niche, and not very competitive.
What is interesting, is sites that link to us appear favorably in the listing, but our site is not found unless I type the title of our homepage exactly.
We are not using 301 redirects, as we are running on an IIS server, and putting a 301 redirect will create an infinite loop, of reloading the home page, unless we have two separate sites (and thus pay for the two separate sites), instead of the two domains pointing to the same IP address and directory structure.
Only our home page is indexed, as we run an dynamic site with a complex URL query string. We are working on going static this winter.
Will this problem go way on its own? If it does, how many google update cycles before things return to normal? Is this a strictly a duplicate content penalty, or are their other factors?
Could this also be a sandbox issue, as the widget.com might be consider a new entry despite being an alias for widget.ca?

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