Facebook User id

If you're using different applications for your website and mobile site, then this is the correct behavior. JFBConnect supports the newer Graph API v2.x. However, if users authenticated when your app was using Graph API v1, their accounts will always return their actual Facebook ID.

The whole purpose of app scoped IDs is to not allow you to track users across multiple apps. If you need to, you should either use the same app for both or you'll need to implement Facebook's Business Mapping API to cross-check user IDs across your apps.

I hope that helps explain, but if you need anything else, just let me know.

Thanks,
Alex

To reconfirm, we are using the same facebook app in JFCB on the web portal and in the Mobile app.

If you're using the same FB App ID and Secret key, the same user ID should be returned from Facebook for each user.

By different applications do you mean different facebook apps or different apps like jfbc and something else ?

No, I meant Facebook Applications.

According to Facebook's own policies and what we've seen, the user ID should always be the same once its set for a user. You can read more about the initial announcement of App Scoped Ids below:
developers.facebook.com/docs/apps/upgrading
Specifically:

No matter what version they originally used to sign up for your app, the ID will remain the same for people who have already logged into your app. This change is backwards-compatible for anyone who has logged into your app at any point in the past.

After April 30th whether we will get the app scope id for new registered users in our website, if so is there any way to get the app scope id now.

Go to the Facebook Developer Area , click into your app and go to Settings -> Migrations. Then, enable the "Use Graph API v2.0 by default" That should do what you're looking for.

I hope that helps,
Alex