When you change USB hubs (multiple ports are connected to each internal hub), the USB device gets a new ID. We use that ID, which allows multiple instances of the same device to work in Aces High.
So if you plug your stick in and see Windows telling you it installed the software for the device and it is ready, then the device got a new ID and you will have to reprogram it.
I am out of the office until next week, but there may be a way to manually edit the config files with the new ID and thus allowing your settings to continue to work.