I finally got to the point where I've gone to Murkmire to quest. I'm almost done with the main quest, have done most of the secondary quests I could find, and pretty much cleared the map (all points of interest, wayshrines etc..). I haven't seen a single Psijic portal so far.
How was your experience with them in Murkmire? Did you see/interact with any of them there?
My seat of the pants observation (i've been doing a *lot* of zone mapping):
It seems there is a fixed (and fairly low) number of Psijic Portals per zone that can be active at any given time.
Meaning, the larger the zone, the less likely you'll be to run into a portal.
There are several small zones where i can run a farming route and consistently get portals during my runs.
No such luck on larger zones ...
PS: And yes, they share the spawn locations with rune stones