It's most likely a driver issue. A WinModem is different than regular modems because it doesn't contain a chip to tell it what to do. It simply relies on Windows to tell it what to do. This is why it's pretty hard to get WinModem's to work in linux.
So what I would think is that in some way, the NT structure is just different, and effects the way that windows talks to the modem. However installing the correct driver should correct the problem all together.