Thanks! I was able to get it working using Knossos 0.15, with a small workaround. I'm happy native multi-controller support is now in FSO!
At first, no matter how I configured the controllers in Knossos 0.15, upon launching FSO, it would only recognize one controller (JOY0)
I was able to get it to work by setting up the configuration, saving, then unplugging the undetected stick, launching FSO and plugging it back in.
I was now able to assign functions to both sticks (MS FF2 for main flight controls, and Thrustmaster HOTAS X for throttle and more buttons)
Unfortunately, I lost force feedback as part of the Knossos 0.15 install, it still works with other games so it's not a hardware/windows issue.
Force feedback previously worked in FSO using the wxLauncher, but it no longer works, even when removing the second stick.
When originally installing FSO I had to update the SDL2.dll in order to get FF working, but it seems Knossos 0.15 uses another version of this, could this file be the problem?
Here is my fs_open.ini
[Default]
VideocardFs2open=OGL -(1920x1080)x32 bit
TextureFilter=1
Language=English
Joy0GUID=5e041b00000000000000504944564944
Joy0ID=0
Joy1GUID=4f0408b1000000000000504944564944
Joy1ID=1
Joy2GUID=
Joy2ID=
Joy3GUID=
Joy3ID=
CurrentJoystick=0
CurrentJoystickGUID=5e041b00000000000000504944564944
EnableJoystickFF=1
EnableHitEffect=1
SpeechVolume=100
SpeechVoice=0
SpeechTechroom=0
SpeechBriefings=0
SpeechIngame=0
SpeechMulti=0
NetworkConnection=LAN
ConnectionSpeed=Fast
LastPlayer=Bonto
[Sound]
PlaybackDevice=OpenAL Soft on Speakers (Realtek(R) Audio)
CaptureDevice=OpenAL Soft on Microphone (Realtek(R) Audio)
EnableEFX=0
SampleRate=44100
[ForceFeedback]
Strength=100