The voltage input for the PCMCIA CAN card powered internally is 5V . If you are measuring the output ( CAN_H and CAN_L)using a Scope, this should be the same for the PCMCIA card if placed in a PCMCIA socket or placed in a PCI- PCMCIA controller socket ( when in your desktop).
Are you using high speed or low speed cables?
Also how different is the output between the 2 setups?