I don't know of a good way to find this out after the fact.

What I would do in your situation is look at their Google Analytics (or whatever analytics package they have) and look at the organic traffic and see for yourself what type of change has happened in terms of traffic and associated organic keywords.

I can't make a judgement on it, but you might check out Graywolf's recent post this month on masking affiliate links. http://www.wolf-howl.com/affiliate-marketing/how-to-mask-affiliate-links/

http://www.seomoz.org/blog/wrong-page-ranking-in-the-results-6-common-causes-5-solutions

Rand talks about six commons reasons why the wrong page is ranking in the SERPs and how to fix it in this post.

I think you may be seeing Roger/OSE still finding some downloadable files and considering them to be links and messing up your OSE reports. Check out what one of the OSE engineers had to say on this similar thread. http://www.seomoz.org/q/competitive-edu-research-via-open-site-explorer.

I'd advise you not to panic, but instead email [email protected] and ask if this what is happening in your case. They also need the feedback of which domains are still showing problems after this latest update.

If you're still looking for advice, you might want to ping @graywolf on Twitter. I believe I see him talking about having a lot of WP sites and he might have some experience or words of wisdom to pass along.