So I've been Magical Keepsake Boxes in my shop for about two weeks and I've noticed from time to time, in my shoplog, it will say I've sold less than I actually have... I sold 13 boxes so far and right now shoplog says it's been 10. It also shows less sP, of course, although I don't know if it also changes the profit (haven't kept track of that).
For some annoying reason, the shop log groups items sold, even on different days...so if you sold some of them too far apart in days, they will be in separate 'logs' in your shop history. Somewhere way back you might find the remaining 3...I'm guessing this anyway, from the way I know it works.