Have you tried clearing all of your apps on the device? I know you mentioned a master reset, but Google will backup your apps, so this would need to be a full uninstall of apps.
Typically the steps you have mentioned ARE a fix, so that's about the only other suggestion I have.
I'm having the same exact problem with my Nexus 6. I am at my wits end with it because I have tried everything. Factory reset, reflashed stock ROM multiple times, got new sim chip, even got a new Nexus 6 via RMA because I thought the radio had died in the phone.
The original ROM that gave the issue was Android N beta and this issue introduced itself after a month of use on N. Factory reset didn't help. Reflashed N beta. Didn't help. Reflashed Marshmallow. Didn't help. New sim chip. Didn't help. New Nexus 6. Didn't help.
I think I have gone above and beyond clearing the app data and all the other steps above.
I'm on my Nexus 5 now with no issues but I'd like to have my 6 back.
Someone must have an answer for this.
Try booting into Safe Mode and see if the message goes away. If it does, it is not the system causing the error but rather a 3rd party app that you installed.
Also try resetting app preferences. (Settings > Applications > Reset App Preferences)
I reset the app preferences and that seemed to have helped the issue. However, after I restart the phone the pop up happens a couple more times but then doesn't pop up again until the phone is restarted again.
Strange. I'm starting to think that an update to the Android phone app is what is causing this issue.
Thanks for your input.