Thanks for the report! I haven't heard of this specific conflict before, so will run some testing on my end.
Could you enable Debug Mode within WP Super Cache, duplicate the problem, and send the results to us via https://jetpack.com/contact-support/ (please mention my name and please don't post it here as it could contain data not suitable for public consumption).
Marking as resolved so we can track the issue via e-mail with the debug log.
Thanks!