Occasionally the Niantic servers give this misleading message - what it should usually say is "Failed to check account status - please reload to try again". IITC will, in most cases, retry for you.
Sometimes this is caused by server issues, and no ammount of reloading will fix it. Come back later and try again.
However, another reason for this message is your account being blocked/suspended by Niantic. There are no (known) cases of this happening due to IITC use, but any use of bots, unofficial (e.g. iPhone) clients, or other ingress mods could lead to this. In this case, the scanner app will also fail to work correctly.