Hi Patrick,
We have the same problem here. What we found was that even though inventory is set to NOT allow negatives, manufacturing will still allow the planner to "override" when he releases the MO. We have the system set to auto-allocate on MO release. So, we've trained our planners to never use the override option and the problem has been minimized, though not completely resolved. I do run reconcile at least weekly even though it takes several hours because of this. Note that we are also using multi-bin, which I attribute most of the problem to (rightly or wrongly).
-Trevor
