Dave, first check for two things. One, make sure the hydraulic fluid level in the reservoir for the mechanism has the proper charge. Two, are you using the top with battery power only? Sometimes battery power isn't enough to operate the top and the top will fault.
Once those two check out, you should read the fault codes for your top. You use the same code reader that you should have for the Pin 8 and Pin 14 engine diagnostics.
Codes for the Cabrio Soft Top (CST) are accessed at a 4-socket connector (X11/12) at the right passenger footwell. From the inside, it's under the carpet against the firewall and under the steel panel. To avoid the need for an extension cable, connect the black lead from the code scanner to any good ground and the red lead to a battery + source inside vehicle.
For a list of codes and their meaning, go to page 65 in the following link below.
http://www.geocities.com/MotorCity/Downs/1039/mercedes/cs1000_mb.pdf