Did you do a full reset or a partial? A partial is to try and keep your personal stuff on the device. If you did that one, it really doesn't reset it enough to fix any system problems. Only a full "Hard Reset" would do that.
Now that popup, it happens, you an just close it. It will likely show up a few times and then finally stop. If you can access everything then you can use it as normal. If, however, the device is still giving you problems, I would suggest taking all your personal stuff off of it and saving it to a google account or computer, then do the "Hard Reset" to completely reset the device.
NOTE: Doing this will clear 'all' the data on your phone, so it is suggested you not choose this option unless you have to, or aren't...