The advantage is that the actual settings during system operation are predictable and known beforehand. The handling of ISA-PnP devices is about to change in Linux v2.2, though. Of course, you need root access to perform these steps. Check which cards are installed and read their documentation. In case of problems consult the vendor of your computer.
Some card has a hardware defect.
Check if all the cards are correctly plugged in. If you can, test the correct funtioning of the cards under another operating system. Often a DOS setup program is provided with the card which allows to switch between these two modes. The fact that pnpdump detects the ISA-PnP cards installed in your system does not necessarily imply that these cards will be supported by Linux. If anything goes wrong, just re-create the file with pnpdump as described above.