Hello John
The CS16600 controller cards incremental encoder channel inputs can accept signal from an incremental encoder with single ended or differential outputs. With typical single ended you will have an A+, B+, and possibly an index or I+ outputs. With differential you will have A+, A-, B+, B-, I+, I- outputs.
For the CS16600 confirm the CARD setting under GENERAL SETTINGS in SETUP is set to MAGIC.
Confirm the wiring again for your encoder type per the CAMSOFT INSTALLATION GUIDE.
Confirm that the outputs from the Yaskawa encoder are standard incremental encoder outputs and not tachometer output signals.