Dunno if this is why its happening, but two things may be an issue wrt the audit:
1) you can audit something immediately after you INF it for SFS. However, sometimes there is no way to say how much of x you "have on hand" and other orders might be waiting with x. If you audit, then someone INFs x after, it adds however many eaches back to on-hand counts, thus making your audit bad
2) OPU carts have to be completely finished before auditing. If you audit while picking, or even packing a cart, it will go to zero and then dump however many eaches back into on-hand when you press Ok on Batch Complete.