Also just booted up and it's taking the wrong usb devices as flight one and two and I can't use my mouse unless I hold down the middle mouse button.

EDIT:

Okay, the TD;LR is that if you have lots of USB devices, and specifically the Thrustmaster MFD #2 plugged in then the game won't recognise all the correct HID devices and can even break mouse support.

However, that's not 'quite' the problem; the problem is the order in which USB devices are registered in windows.

I found this app: https://theairtacticalassaultgroup.com/forum/showthread.php?t=13009

called JoyID, which allowed me to re-order the devices so 1 = stick, 2 = throttle, 3 = rudders, and then the two MFD's and upon relaunch, Squadrons sees the first three and doesn't break now, even with the MFD #2 plugged in.

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NEW EDIT:

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So, I've found the problem, for whatever (crazy) reason, the devs filter out HID Devices that don't have an X axis. That means some rudders which have a ROT X axis aren't seen.

The solution is to use the firmware update software with the rudders to add an X & Y axis to the rudders but obviously not bound or mapped to anything; just that the firmware reports to 'Windows - Game Controllers' as having them.

Save and update the firmware and now the rudders are seen 100% of the time.

If, like me, you have VKB rudders, you can see some screen grabs showing you this at:

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https://answers.ea.com/t5/Technical-Issues/FIX-for-VKB-T-Rudders-first-post-removed-by-mods-as-spam/m-p/9668738#M3931

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Hope this helps