Think I may have found a problem with site. Can you confirm my suspicions?

[IanTheScot]

So I've been wracking my brain about a problem. I had posted earlier about our degrading rank that we haven't been able to arrest. I thought we were doing everything right.

Many years ago we had a program that would allow other stores in our niche use our site as a storefront if they couldn't deal with setting up their own site. They would have their own homepage with their own domain but all links from that page would go to our site to avoid duplicate content issues (before I knew about canonical meta tags or before they existed, I don't remember).

I just realize that we had dozens of these domains pointing to our site without nofollow meta tags. Is it possible that this pattern looked like we were trying to game Google and have been penalized as some kind of link farm since Panda?

I've added nofollow meta tags to these domains. If we were being penalized for this, should this fix the problem?

[IanTheScot]

So, no one has an opinion?