I don't even know how many times I've played this game through to the end and every single one of those times, after getting the last rune and going through the last portal, it dumps me back at the beginning. The only change being that the entrance to the last level is blocked. I have never once been able to get to shub niggurath. I know for a fact I got all the runes. What the Hell am I missing here???

There's a new path open in the main hub once you got all the runes. Go down the stairs and fall down into the teleporter.