Solution:

We are terribly sorry that the old User Manual and old PCB PCM-3540R REV. A1 01-1, 01-2, 01-3 have printing error. New User Manual is on http://support.advantech.com The connector assignment should be: 1. 44 pins connector is CN3.. 2.. 16 pins connector is CN6. 3. CN4, CN5 are 3 pins and correct.