Homepage and Category pages rank for article/post titles after HTML5 Redesign

[mcluna]

My site's URL (web address) is: http://bit.ly/g2fhhC

Timeline:
At the end of March we released a site redesign in HTML5
As part of the redesign we used multiple H1s (for nested articles on the homepage) and for content sections other than articles on a page.

In summary, our pages have many many, I mean lots of H1's compared to other sites notable sites that use HTML5 and only one H1 (some of these are the biggest sites on the web) - yet I don't want to say this is the culprit because the HTML5 document outline (page sections) create the equivalent of H1 - H6 tags.

We have also have been having Google cache snapshot issues due to Modernzr which we are working to apply the patch. https://github.com/h5bp/html5-boilerplate/issues/1086 - Not sure if this would driving our indexing issues as below.

Situation:
Since the redesign when we query our article title then Google will list the homepage, category page or tag page that the article resides on. Most of the time it ranks for the homepage for the article query.
If we link directly to the article pages from a relevant internal page it does not help Google index the correct page. If we link to an article from an external site it does not help Google index the correct page.

Here are some images of some example query results for our article titles:

Homepage ranks for article title aged 5 hours
http://imgur.com/yNVU2

Homepage ranks for article title aged 36 min.
http://imgur.com/5RZgB

Homepage at uncategorized page listed instead of article for exact match article query
http://imgur.com/MddcE

Article aged over 10 day indexing correctly. Yes it's possible for Google index our article pages but again.
http://imgur.com/mZhmd

What we have done so far:
-Removed the H1 tag from the site wide domain link
-Made the article title a link. How it was on the old version so replicating
-Applying the Modernizr patch today to correct blank caching issue.

We are hoping you can assess the number H1s we are using on our homepage (i think over 40) and on our article pages (i believe over 25 H1s) and let us know if this may be sending a confusing signal to Google. Or if you see something else we're missing. All HTML5 and Google documentation makes clear that Google can parse multiple H1s & understand header, sub & that multiple H1s are okay etc... but it seems possible that algorythmic weighting may not have caught up with HTML5. Look forward to your thoughts.

Thanks

[blu42media]

Check out this previous post right here on moz:

http://www.seomoz.org/q/html5-multiple-h1-tags

[mcluna]

Thanks for the note. I had read that post. I think the distinction here is that we're now seeing it in the wild vs speculating on how Google might handle them and what they recommend.  We are going to test going back to distinct H1s to see if it corrects the issue. If so then we finally will know that Google is still a bit confused when handling multiple H1s (as many as we have at least) as per HTML advanced specs. Bing is confused in similar but slightly different way.Indexing the wrong pages also.

Thank You.