The cable was connected to a PD power source, and somehow that doesn't work. After connecting the cable to a non-PD source, the E-mark tool starts normally so I can exit the tool.
The manual for the CT-3 states that you should not plug the other end of the cable into anything to get the e-mark data. They also recommend to power the unit from the PC port (can plug it into a power bank and not a PC of course for power).