Please be aware that the ADC on the FMD/Fx/Nano PLCs is a 12-bit ADC. The older T100MD had a 10-bit ADC.
If your ADC readings with the FMD are about 4x too high, the then differences in the ADC circuitry are the root cause. You will need to modify the CF that read the ADCs to accommodate the extra 2 bits of resolution. You could just divide the new readings by 4 and then just use the old code from that point forward.
As I am sure you have noticed, the DB15 connector is wired a bit differently between the generations of PLCs. If your analog circuitry is dependent on ground reference or 5V ADC reference voltages you have a good chance of being wrong with your old cable. There is a only one pin for each signal on the FMD vs. 3 pins for each on the T100MD88.
TRI has a PDF on differences between the old T100MD and the FMD boards here:
http://www.triplc.com/documents/FMD1616-10_Upgrade_Notes.pdfThe other differences have to do with the amount of DM memory and non volatile memory. There is less of each on the newer FMD boards. If this poses a problem, the add-on RTC-FRAM module is what I use to get back these resources.
Best regards,
Gary D*ckinson