I am at a loss. Some where there is a restriction in plumbing and there is a pocket of air that gets pressurelized. Once the pump turn off the path of least resistance is back through the skimmer lines. To pop off the skimmer lids that would be a good size air pocket or some pretty high pressure. Maybe all the return lines are collapsed? I am guess everything visiable is fine. Back flowing through the pump is pretty resitictive, I can't imagine backflowing enough to pop the skimmer lids off. Maybe the filter is almost completely filled with air?
How about some photos of the pool, spa, plumbing, etc and a video of the lids popping off.