Hey Douwe,
I have tested this several times with PCI devices, and I have never ran into a problem. I can run the analog output and analog input examples at the same time, restart one, or stop one and never have a problem. It is possible that this is cuased by the interrupts that the PCMCIA devices use, because they do not have DMA. Try opening the LV Cont Acq&Graph(buffered) example and the Continuous Generation example and let me know what happens. You should be able to run these two VIs without any problems.
I hope this helps.
Joshua