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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 help@seomoz.org 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.

Thanks, that webinar and powerpoint presentation was great. "You can't outsource giving a shit" - Tom Critchlow lol