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Logitech software won't work in a Third Wire game. You should use the Options. I have had some "funny" events using the software also.
When you go to the Options>Control page, you can see a pulldown menu on the right page beside Keyboard Control Map. What is in that menu? There will be a Default. Anything else? Are YAP controls in there? LogitechX3dPro? SaitekX52? Just checking. We include those as a starting point.
When you open Customize... What file is opened? Can you see? Is it Default.
Then when you try to click Button 7 at the Autopilot spot, does it show you have clicked it? Do you first click on the item with your mouse before clicking Button 7?
I don't imagine this is the problem but sometimes I have to click a switch several times for it to get the idea...especially with the Hat switch.
Anyway, tell me what happens. Maybe I can figure it out.