The difference in the rates is the amount that the agency is pocketing.  Some agencies may be willing to negotiate the rate a bit but since that is their income... well, not all will.  It probably depends on how good a client you are with that agency or how badly they want the booking.

That's one of the reasons why I usually recommend to newbies to find a good agency and stick with that one as much as possible.  You build up a rapport - they know what you like and can steer you away from girls that aren't your type or won't show you a good time - and since you're throwing business their way on a regular basis, they may be more willing to match another agency's rates and take a bit of a loss on a date now and then to keep your business.

Some agencies though are just in it for the money, and don't care about client happiness or loyalty.  They're the ones that won't lower rates, or do anything beyond book the date for you.  As long as they get the money they want, they don't care about the rest.  They don't even care if the date actually happens.  They've got your money and that's all they care about.