Two links to the same destination on the same page is unlikely to be the cause of your problems. When Googlebot sees a second link to another page, it completely ignores it:
- It doesn't pass extra Pagerank to it
- It doesn't associate the anchor text of the second link with the page
From my testing, Google treats the second link pretty much as if it didn't exist.
The one exception is if the second link has a different fragment identifier. For some reason, Google treats these two URLs as different when they are both linked in the same page even though they necessarily both link to the same document:
You don't want to use
nofollow in this situation. In general,
nofollow should never be used on internal links (links within your site to your own site.) More specifically in the case of duplicate links, when you
nofollow one of two links to a destination, Google treats both links as if they were nofollowed. Their logic is that if the link is marked as untrusted in one place, Google should treat all instances of it as such.
Your new theme may be causing SEO problems somehow, but the mechanism you propose has nothing to do with it.