It's not uncommon. Often I see that it is paid at close and not up front. I know of a couple agents though that do this because if you search for 6 months for houses with them and then never buy it's the only $ they get out of showing you homes for 6 months. I doubt it's per house. I would just pay it and if you don't feel your agent is doing their job well then go to them and say so. If they don't cooperate, go to the broker. Then remind the agent that you will be leaving reviews all over. I don't know a single agent who would trade bad reviews for $595.
The only problem with this is if the agent isn't worth it. Otherwise, you want a professional agent and someone who values their time often (not always though) brings value to the table.
As far as the difference in 3% and $2000. Is it an issue for you? Will you be buying houses that don't meet the $2K cut? If not who cares. If so then talk with your agent. Let them know you plan to buy several houses over the next few years and you want to build a mutually beneficial relationship. I work deals with investors I work with because I will be working with them for many years. Heck if they are an amazing agent and get you a better deal than you thought you could get make them get an extra $2k out of the sellers price to cover the commission.