Well, I'm more of a functional guy, and so far I found BaanERP calculation of WIP to be quite accurate. And I have to be honest, you're not providing enough data from your case explanation for any diagnose to be accurate. Let's start with one thing. You said,
"At the start of the order, the WIP value is the sum of all BOM items of 123, which adds up to $ 400.00 per unit. Total WIP at this point is $ 40,000.00"
Well, actually at the start of production order, the WIP contribution of the particular order is 0. Only after you start issuing materials to production floor will your WIP contribution go up. I assume you mean to say that you've issued every single materials of the production order early on in its progress (which means you'd also have issued the box at the beginning of production order)? And the sum of costs of all those materials come up at a round number of $40,000? Sounds unlikely
Francesco, if you could post a more thorough explanation of the case, then I might be able to help a bit more. Don't worry if the explanation will sound complicated, nothing is simple in accounting anyway