I noticed during testing that sometimes portal would take a long time to appear if they did at all. The files posted do not contain a respawn interval or anything like that, just a location and ID. I'm sure we'll figure it out in the near future, really only an issue in PP if you have a train and can't use a gate to lose them :)
I know the dungeon mobs are the weaker versions, I'll get those fixed eventually if no one else does it first but it's pretty far down my list.
edit: As far as I know, most of the files are the same ones used currently on the official servers so I'm 99% sure the issue is elsewhere.