Since upgrading to the new 4.0 OS my users want the phone call notifications (missed calls, recieved calls) back in the email window. Are they located somewhere else now? Any one know where they went or how to get them back without downgrading OS back to 3.7?

It's a setting that you have to change.

4.0 defaults the call logging to none. Change it by going to:

Phone/options/call logging/select missed calls, all calls or none.