I don't recall hearing of the same problem on a B&S engine before, Ross. If I just go by what you posted, the problem appeared when you clamped on the crankcase cover, so most likely something was being squeezed axially. Without knowing whether it was part of the camshaft system or part of the crankshaft system, that is about as far as I can get - but since it appeared without provocation and suddenly disappeared when you dismantled and reassembled the engine, it may be that something has excessive slack axially, allowing something else to fall into the gap at times and jam everything. When you took the cover off, there was no axial constraint so it was free. When you put the cover back on with the wrong bit still in the gap, it jammed again. When you juggled everything around a bit, whatever it was fell out of the gap - for now.
