So is ACCPAC supposed to.
I believe the problem is that often when using FIFO/LIFO it only appears that the quantity on hand of an item is zero and the cost is zero. Actually there may be two (or more) lots for that item which net to zero, but one is positive and the other is negative. The system will use Lot 1's cost (LIFO) or the last lot's cost (FIFO) when you ship negative.
If you find this to in fact be the problem, and you want to know how to quickly collapse such offsetting lots, let me know and I will give you a trick. It won't find such a problem, but once found it will clean it up.