Hi cjsamples,
I think our software/documents over use the word channel which causes confusion. There are Motor Axis Channels, DAC Output Channels, and Encoder Input Channels which are all different things.
Any KFLOP Motor Axis Channel can be configured to make use of any DAC or any Encoder by specifying the Input and Output channels. See:
Configuration Screen
The KanalogInitialPID.mot file is an example of a Kanalog Axis using DAC #0 and Encoder #0. It seems you are loading it into multiple Motor Axes Channels so multiple axes are all trying to use DAC 0 and Encoder 0 as their I/O devices.
For your Second Motor:
#1 select Axis Channel #1
#2 load the KanalogInitialPID.mot configuration
#3 Change the Input Channel and Output Channel settings to the Encoder and DAC you want that motor to use (ie. #1 and #1)
HTH
Regards