Are you using the Joomla Update manager, or the update tool built-in to JFBConnect?
Either way, if the automatic update process isn't work, I'd suggest downloading the main zip package from the My Downloads area in the top right user menu. Once you have that, install it using the Joomla installer like any other extension and that should upgrade your main component automatically.
You'll also want to update any modules or plugins you are using to make sure they are at v5.0 as well. You can check all your version numbers from the JFBConnect Admin Overview page.
I hope that helps, but if you still have issues, just let us know.
Thanks,
Alex