Have you NEVER seen CM's do weird things? We have one customer who has had at least 4 instances of them updating with positive amounts, even though the lines updated correctly, thus an out of balance DTR.
I've blamed it on user input - as @JeffSchwenk said, it is confusing so they usually enter negative quantities and/or negative pricing (I've seen them do both!) and it never comes out clean. I'm guessing in this instance, they entered it incorrectly then corrected it but it only half corrected it.