I am facing a special problem with the newest FRED Open(Why don't I have any of the older ones when I need them

):
It is supposedly related to the -mod parameter or the whole mod-controlling system. When I open FRED and start making a mission, nothing happens yet. I can do things normally, even using any mods or new craft, but when I save my mission, it says it cannot find the POF files for the mods. It is interesting since I am pretty certain the mods are there, and it is more interesting that FRED had been able to read any kind of mods before saving.
It does not happen with only official things, only with non-canon models. I haven't tried putting the models into a .vp, though. I don't think that would be the solution. Has anyone encountered this problem?