Unfortunately, the FMC we use is not fully compatible with FS2004. This means that a little trick is needed to import FS flightplans into it.
1) Create a file called "FS2002.cfg" in your FS2004 main directory. The content of this file doesn't matter at all, it can also be empty). The existance of the FS2002.cfg let's the FMC detect an FS2002.
2) Copy the flight plan files you want to import (file extension ".pln") to FS2004\Flights\MyFlts. Create this directory if it doesn't already exist.
That's. Now, the FMC will be able to detect and import your flightplans.
EDIT: It seems that the FMC isn't able to import every FS2004 flightplan. For now, we don't the reason for this behavior and thus can't offer a solution. Until we can come up with a solution, we stronly suggest to use the FMC as it is meant to and to avoid the flightplan import.