After flashing the N9 it worked for about a week or two and then I started to get the message "Phone not allowed MM #6" I never had this before and I've had the phone for a year now. I have not idea what is going on... It's so strange! How can I fix this and why did it happen after I installed the firmware update?

your imei is blacklisted, or perhaps melted.
check your imei is good (*#06#)
call customer care of your carrier.
I suppose its legally purchased.