Sometimes they appear to not understand what they are doing.
I think the problem has been that historically, no-one was stopping them from making up things on the spot. Listen to the stories from people dealing with bureaucracy in communist times - the bureaucrat was powerful and could insist on anything if he/she felt like it. Nowadays, of course they aren't powerful - but I get the feeling that the mentality lingers on in some places.
As you say, being firm is the best approach - let them know that you know the law, that the law is in front of them and that if they don't accept the application, they'll be hearing from a solicitor in due course. The instinctive Polish reaction ("****, must cover my ass, what if he's right?") kicks in and they'll accept it ;)
The problem is also further caused by the lack of clear guidelines - for instance, Poznan demands that you give over a bank statement showing sufficient funds to support yourself. If you ask them what they think is sufficient, they don't actually know themselves - it's entirely up to the person on the day. There are no guidelines (that I've found or seen) to actually say what is enough money for an EU citizen to not need a work contract.