Probably, as it seems this hack affects the wp_options table to inject the links into search engines results and may have altered a few other things in there. Did you restore this table when you reinstalled WordPress?
I checked your site and things seem to be working alright. I need you to do something for me to make sure WPP is updating the views correctly into the database:
1. Open wordpress-popular-posts.php using an editor such as Notepad or Adobe Dreamweaver.
2. Find this portion of code:
3. Change it to:
4. Go to your site and view any post / page. You should get an alert saying something like "OK. Execution time: XXXXXXXXX". If so, WPP is working fine and there must be an option or setting that's different from your original configuration.