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'03 SL500's Tanzanite Blue, Aegean Blue, Mars Red, Alabaster White '11 S550 Flint Gray
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When you start to lower the roof, the front windows should drop slightly and the rears should go all the way down. The roof controller requires that all four windows are in the proper position before proceeding with opening the roof. In order to know the position of each window, they need to be normalized, and the two door controllers must be communicating to the roof module. The roof module controls the rear windows directly.

Since you were working in the trunk. I would also check the switch/wiring on the trunk lift cylinder near the left taillight. It needs to register as fully up before the roof will start to lower. The plastic rod is easily broken, or the wires may have been damaged.
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