Here is one thing that messed my iPad up when I moved to iOS 5. I like using the switch on the side to "Lock Rotation". When I first upgraded to iOS 5 beta, some apps had sound and others didn't. I did a "Full Reset" to get it working again, but I think I now know what the problem was. The original function of the switch was only to Lock Rotation. In one of the later versions of the iOS Apple had changed the switches function from Locking Rotation to Mute. Then when another future update came out that allowed us to have the option, I moved it back to Lock Rotation. Now when I went to iOS 5, I believe that it thinks that the switch was being used for "Mute" instead of Lock Rotation. I would bet that if I had changed the switch setting back to Mute, toggled the switch back and forth to mute, then un-mute, then the sound would have worked. I could have then change the switch back to "Lock Rotation" and all would have been well. If you have your switch set to Lock Rotation, give that a shot and let me know what happens?
Also a note about the "In Notification Center" vs. "Not in Notification Center". Whenever you go into an app, the top row says "Notification Center". If it is "ON" then it will be "In Notification Center". If it is "OFF" then it will be in the "Not in Notification Center" section. For Time Master, it doesn't matter if it is On or Off as we do not use the Notification Center. The Notification center is the thing where you swipe from the very top of the screen down to reveal the Notification Center.
Update: I checked the Notification Center on our iPad 2 and sure enough, Time Master was not there. Oddly enough the Badges were working. So I went to Setup -> General -> Audible Notification and changed it from "Off" to "Every 10 min". Then when I went back into the Notification Center, Time Master was now there. So that is how you get it to show up in the Notification Center.