The author of Briss has not posted in almost five years. I believe the project is abandoned. It is open source though, so somebody may pick it back up again.
You can try your cropping using
k2pdfopt and see if it does not have the same issue. To do manual cropping, if you use the MS Windows version of k2pdfopt, select "Crop" for the conversion mode and then check one of the crop regions, put in a page range (put 'o' for odd pages and 'e' for even pages), and click "Select" to graphically select the crop region for those pages. See the attached screen shot.
You can pick more than one crop region, even on the same set of pages. The MS GUI only allows three selections, but using the command line directly, you can enter up to 32.