Hi Kane,

1. What type of e-commerce CMS are they on? - Custom Solution but in middle of migration to magento scheduled for launch in February.
2. Are these mis-matched pages always on the same site (and not the competitive site that you mentioned)? - Yes. There is no overlap onto other domain pages, just the domain that appears to have been dinged.
3. Are there any canonical tags on the site that are pointing towards the other website? - No.
4. Is the content on each page unique for that domain (not including the other domains you mentioned)? - For the most part. We don't duplicate content on same domain, it is really just across domain.

Also, forgot to mention.  Bing and Yahoo rank this domain favorably, and is usually on Page 1 for competitive keywords. This appears to be a Google only related issue.

Update:  I tested copying and pasting unique sentences from category pages in Google and everytime it did not return a search result.  When I test search using site: example.com, the page is returned.

Could this be a combination of supplemental + panda?  We have not received any penalty/message from Google (yet).

Over the past few months we have been chipping away at duplicate content issues. We know this is our biggest issue and is working against us. However, it is due to this client also owning the competitor site. Therefore, product merchandise and top level categories are highly similar, including a shared server.

Our rank is suffering major for this, which we understand.  However, as we make changes, and I track and perform test searches, the pages that Google ranks for keywords never seems to match or make sense, at all.

For example, I search for "solid scrub tops" and it ranks the "print scrub tops" category.

Or the "Men Clearance" page is ranking for  keyword "Women Scrub Pants".

Or, I will search for a specific brand, and it ranks a completely different brand.

Has anyone else seen this behavior with duplicate content issues?  Or is it an issue with some other penalty?  At this point, our only option is to test something and see what impact it has, but it is difficult to do when keywords do not align with content.