JFBCSystem plugin is indicating that it is activated but not detected.
Where are you seeing that message? Mainly, go into Autotune and in the Site Check area. That should properly detect what things properly and if it's showing disabled there, you can enable it.
As for issues, we don't have direct integration with JomSocial Profile Types or some other extensions you mentioned. However, things should still work fine with JFBConnect with those extensions. If you're having issues, can you let me know what they are, and we'll gladly help however we can.
Thanks,
Alex