Chris,
Ahh, glad you got that going. Not sure why that would be necessary, but there is a lot of communication back and forth between your site and LinkedIn. If sh404SEF alters those links in a bad way, it could definitely cause a problem.
For JLinked operation, we really don't have any front-end URLs except for the registration page, which shouldn't really need to be SEF'd anyways, so you shouldn't have any drawbacks from disabling sh404SEF for JLinked.
If you run into any other issues or need anything else, just let us know!
Thanks,
Alex