Braking is a completely separate system than 2 or 4-wheel drive. What I suspect you are seeing is when in 2-wheel drive, the power of your drivetrain is helping keep your rear wheels spinning, and when you are in 4-wheel drive, power is being equally applied, thus taking a little more power to evenly stop all wheels at the same time. There's more to it as well, such as a proportioning valve that helps adjust the ratio of braking power to the front and rear axles, as well as some systems apply braking to opposite corners in two separate systems (left front and right rear are one system, and right front and left rear are another) to help prevent loss of stopping power should one system fail. I'm afraid I don't know the specifics of the system in the Jeep to tell you what's there.
Did you bleed the brakes yourself? Do you know how to do this? (Does your Jeep have ABS?)
Unless someone here has better advice, one thing you can do is either bring your Jeep to a shop and have them bleed your brakes, or have them test what the pressure is at each caliper.
There's a link on the ever popular Stu-Offroad
page with more information.