What's the full path file name of two of these PDFs with same thumbnail?
The problem is showing in the advanced web interface client, or in the standard one?
If advanced client, try deleting the thumbnails cache, at the c:\MySite\wwwroot\images\thumbs directory.
If you have not installed the advanced client, and have not defined a cache folder (thumbnails configuration panel option), clear your Windows temp folder (type %temp% at the Windows Explorer address bar, to open it)