Yeah, some of the steps needed to make Windows load the WinUSB driver are done during the first time it sees that VID/PID pair - it caches stuff in the registry and never queries any device with the same VID/PID pair again.
From what I've seen, the device manager can be used to delete some of those cached registry entries. For example, after plugging it into the USB 3.0 port and failing to install drivers, I can get it to install successfully on the USB 2.0 port if I first uninstall the device from the device manager.
For any machines where it doesn't think that the device is malfunctioning, could you try looking at the registry entries as I described here?http://stm32duino.com/viewtopic.php?f=10&t=1242&start=10#p15985
Short of getting an actual USB event trace, that would probably be the most useful debugging information I could get.
I can also build a new image that uses a different PID, if you want to try fresh without hunting down more clean Windows installs.