rationalskepticism.org

At early time, the radiation was in thermal equilibrium (maximum entropy) but the paradox is that entropy has increased since then. The resolution of the paradox is that gravitational clumping of matter allows the entropy to continue to increase. Most of the universe's entropy is found in black holes that will continue to grow until the remote future when the background temperature falls below that of the largest black holes and Hawking radiation evaporates them.

Sir Roger Penrose explains some of this in this clip: