The only weird thing im noticing that might help explain my situation is when ive extruded my cubes it seems to create a duplicate of everything, 2 points, edges, faces all sharing the same space.
when i select a point and slide it for example, there is another one in its place. Thats not normal is it?
....... ran some tests. bingo, that was it. wild. Somewhere along the way i was extruding 2 faces at the same time occupying the same space (or so colse you cant tell) and it created a duplicate of most of the faces in the model. So when I was joining edges together, some would be a complete loop and others wouldnt even though they looked like they were, and it was just completly random which ones would connect and which wouldnt.
that .... was maddening. Now that I know ill be more careful in the future.