Can you tell me what numbers you are getting with each meter and how you are determining the CC is incorrect? Also, make sure your camera is in the manual mode, including manual ISO, when using it with the Cyber Commander.
<f1.0 means there is not enough light metered to allow the use of f/1.0 for proper exposure. If f128 appears, you may not see a change if you increase power, as that is the maximum aperture that is readable.
Also note, the Sekonic may be set to 1/3 stop settings, where as the Cyber Commander reads in 1/10 stop increments. So you may see f/9 on the Sekonic but see f/8.0'3 on the Cyber Commander. These are essentially the same reading. Page 42 in the manual will fully discuss this.
http://www.paulcbuff.com/manuals/cc.pdf If you are still seeing way off metering go into Setup>Advanced Configuration>Factory Calibration> use the left joystick right or left to restore factory calibration. If this does not correct the problem, you may want to give us a call, as it may require in depth trouble shooting.