With UCM 220.127.116.11.0 there is a new feature which is "Create System Thumbnails" , where in filter can be set for which content types we need to have thumbnails created . It is under Administration menu .
First of all from Administration - Refinery Admin - File Format - uncheck the file format which you are trying to create thumbnail.
Then from the new menu add the format to be converted .
Then do checkin , I think this does not send the content to IBR for thumbnail creation .