The CKHub reference design was written for both the CY7C66013 (48-pin package) and CY7C 66113 (56-pin package). That's why, to be flexible, the design of the new released application board CY3654D301 Rev A provides both 48-pin socket and 56 socket for the user to connect to the development kit through the flex cable.
One of the internal differences between the CY7C 66013 and CY7C66113 is that the CY7C66013 (48 pins) does not have a DAC port which is used in the current protection circuit in the CKHub design. In other words, if the applications board is used as the CY7C66013 (48 pins), the default of the board disables the current protection circuit which powers off the downstream ports. That's the reason why devices connected to the downstream ports are not detected.
A work around solution is to manually connect the DAC and DAC pins to Vss (DAC and DAC are used to enables the current protection circuit which then powers the downstream ports, these pins are located on J4 of the applications board).
Also, in the option.inc file, you should change the number of maximum ports to 3 because only 3 ports are available on the applications board. Note that after modifying the option.inc, don't forget to recompile CKHub.asm.