Hi,
Please take a look at the following thread:disable message "Your carrier may charge for SMS messages used to activate iMessage"
Go to Settings --> Messages --> slide the switch on iMessage to turn it On (if it is Off) then tap Use your Apple ID for the iMessage then Tap your apple ID then sign it out. The iMessage will automatically turn-off and will stop the annoying pop-up.... It works for me on my two IOS. (Quoted answer from linked thread)
There are a lot of people on this thread with ideas and "fixes" for the issue you are describing, so it would be worth having a look and trying to apply any to your situation.
It could be a Software issue, but i would take a look at the thread link provided before heading down the restore route.