Exactly the same problem was boting in San Francisco (i dont live there) it worked the whole day but now just catch flees. The Bot ist just spinning pokestops and collecting items.
My OG account that had the flee temp ban got perma banned earlier today. No biggie, I started a new account this morning. Blah, it got the flee temp ban after less than an hour botting. No way around it, PokeFarmer is detected.