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I've sent a fix for this to nlight, it should be out as soon as he does a release again.

I have submitted a fix for this to the author and he has merged it without a comment, but no new release yet. He seems MIA for some time now. If it goes much longer I guess I can try and take over maintenance of this project and publish new releases.

Sorry to hear your many problems with the addon. Both me and nlight has been a bit preoccupied lately, so sadly we didn't get all the bugs introduced by 0.90 fixed very quickly. I have just sent nlight a suggested fix for your issue that fixes SAS controls not being overridden on user input. Hopefully he will do a release if he finds the fix satisfactory and once he has time to test it. As for your other issue with presets being deleted every time you start the game, it would help us immensely if you went to https://github.com/AlexanderDzhoganov/ksp-advanced-flybywire/issues and described the issue in detail.

Can everyone with FPS problems, EVA movement issues and unintended SAS-effects please try the new Version 1.4.6 and report back if it fixes their issues. Update through CKAN or go to kerbalstuff

In the new version for 0.90 all axis can be inverted independently. Enjoy!

That's a very valid observation. Axis inversion should be set on a per-binding basis instead of globally. I had the same thought fleetingly when developing the EVA controls. I've opened an Issue on this and will try to get it implemented for the next release. It does touch upon a lot of code, so no promises on when that will be.