I don’t really think so, because if it were a fault with Bow Commander, the disk wouldn’t be readable even in EsxDos (which you said it is). So I reckon that EsxDos does something non-standard with that volume of disk operations, which causes problems for Windows and other operating systems, but not for EsxDos itself, because it’s something it’s designed to handle...
The problem is that, until now, there hasn’t been a programme for EsxDos that would use such a large number of disk operations at once (bulk copying, deleting, etc… and I think this is where EsxDos’s bugs and lack of fine-tuning come to the fore…). I don’t mean any harm by this; nobody writes flawless programmes, but it would be good to fix this behaviour at the OS level… .