I have had to reload settings in CH Manager on many occasions. I usually do it now right before I am going to log in as a habit. It has been that way in AH II for awhile also. Reload once and all is good for the evening.
Ditto, and I have everything mapped through AH, NOT the CH control stuff too.
This little program comes in handy for me at least -
http://www.nirsoft.net/utils/usb_devices_view.html "usbdeview" is the name of the program.
You can view all USB devices, and enable, disable, virtually unplug, etc, all without having to physically plug/unplug your stuff, or switch off your powered hub and such. Some games like Star Citizen and others, if they detect a usb joystick at all, it'll default to it and not let you use mouse control properly, so this program is great for disabling HOTAS prior to jumping into such games where you don't want it. Also, for when I've had Ah2/3 issues of for unknown reasons the sticks not showing up or working, just disabling/enabling them with usbdeview quickly solves the issue for me.