This happens when you set your total items different from your combined storage space. You can just ignore this message or configure your inventory in a way all items adds up to your inventory size. For example: keep 200 pokeballs + 50 potions + 50 Revives + 50 Berries = 350 items.
Try going to a more populated area. Test por example San Francisco or Los Angeles
Try a more populated area and give it some time for pokestops to load. It can sometimes take a while to show.
Zero accounts of mine have been banned since the use of Catch'em. I tried pokefarmer and two accounts got banned.
I have never had issues in which bot showed some date while in PTC was level 1. I'm sorry but there's no way I can help you as I can not reproduce the bug. Maybe you should try creating a new account (Google recommended) and see if this happens again.
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Glad to hear it's working for you now