article2pdf plugin and plunge in traffic on site

Traffic to my site has taken a dramatic plunge in the past few days and using Google Webmaster tools it seems like a lot of my articles are being seen as duplicates – the original article and then the article in cache in pdf format. I think this is sending up warning signals to Google and as a result I’m not being indexed as I used to be. Anybody else experiencing this? My site has been running article2pdf plugin for a year or more and this is the first time I’ve been aware of a problem. Thanks.