With MEDPro the SEGA CD CPU only works in the 4MB version. When using bank-switching, the MEDPro turns off the FPGA SEGA CD core.
Update: To get the FPGA Sega CD acknowledge I had to create a folder called "Prehis", then put a ROM in it called called "Prehis.bin" with a cue sheet called "Prehis.cue" with the following text:
FILE "Prehis.bin" Binary
TRACK 01 AUDIO
INDEX 01 00:00:00
Then, instead of playing the folder like a Sega CD game, I had to open the folder and launch the bin directly. Only then would it detect the FPGA Sega CD core.