GOPs (Group of Pictures) are data structures used in MPEG video consisting of an I frame, B, & P frames. They can be opened or closed, and in NTSC are usually anywhere from 15 to 18 frames. Does Sorenson allow you to customize these settings, or issue a report after encoding?
As long as the frames are correct, optimally the GOPs should be closed. Can you find out if they were closed or not?