Hi,
Although it should be transparent to the PCMCIA card, I have also have had some problems with some adapters. Specifically, I have been able to install the card in a PCI-PCMCIA adapter form Qualtech, but not if I'm using a cPCI Cirrus Logig adapter. We haven't been able to find a cause for this.
If you need a GPIB interface in a cPCI system, you might consider the PXI-GPIB. PXI fully compliant with the cPCI standard.
DiegoF.