We're safe. Thanks for your concern, it is appreciated.
As to your issue, I'm not really sure what we can help with here. If they put your app in review, there's nothing we can do about it. It's definitely not something that simply having JFBConnect causes to happen as the majority of apps do not get flagged by Facebook in general.
I know you mention there are "some options which are not included in your guide". That does happen as Facebook is
constantly and annoyingly always updating their app creation pages. We're always trying to stay on top of it, but they slip things in sometimes. If there's something you can't figure out or have questions about though, please don't hesitate to let us know and we'll gladly help provide whatever details on how it should be configured.
As for having the plugins disabled, that simply would prevent any JFBConnect functionality from working on the front-end of your site. Autotune can run and setup your app in the admin area even without our plugins enabled. As noted though, just running Autotune shouldn't flag your app in any way. They have an API for configuring apps for a reason.. they want tools to set them up automatically
Thanks,
Alex