I have yet to try it in any games as I think Windows is having issues as it does read as 2 joysticks.
I'm sorry to hear about the problems you're having. This probably isn't a "problem" though, & if it's anything like my Warthog, that's how Windows will see the devices, as they each have their individual USB cable & device ID.
It shouldn't be an issue in newer games, such as DCS World, ARMA, & so on, but older software - like the old Wing Commander, X-Wing & so on - will only see one of the two devices, the one that is set as the default device under the Advanced tab of your game-controller settings in "Devices & Printers".