Assuming you are using Ultimate SEO to rewrite your pages. Don't rewrite your popup_image file because even if you block it in your robots.txt file it will still get spidered which I believe is causing a duplicate content penalty of some sort. Also add <META NAME="ROBOTS" CONTENT="NOINDEX, NOFOLLOW"> to your popup_image file. Doing this got all my pages back into the index for the first time in three months.
