Odd issue with homemade rotary encoder panel, using Leobodnar board

[Hoirtel]

Hello, hoping someone here might be able to help with a strange issue I am having. Not so long ago I made a home controller with a leo bodnar board, this is a box with 8 rotary encoders, all with push. This is the second controller I have made, with the first all switches and I made some time ago.

I can't say when exactly the issue happened, or if it hasn't always been present, since I do swap airframes a bit. So this controller is working as expected in windows game controllers options, and works as expected in all module controller binding screen. The really odd thing is that is some modules, only two of the controls work? In the apache and hornet, they all work as expected. In the harrier and F15E, F5 only two work in cockpit. Totally bizarre. The harrier I also have two push buttons on the other leo board do the same thing, and in the F15 one half of my middle cougar thrust master screen also does not work, although sometimes it starts during the flight. 

I really can't work out what would be the source of the problem? I have focused some trouble shooting on the main rotary box where I tried removing and re-adding it and also moving it from USB hub (powered) to a native mobo socket. No change. The affected aircraft controls do work when rebound to a different switch on another controller (throttle/other box).

I wondered if it was the way I built it, or something to do with the components but why would it works so flawlessly in every single control menu and in some modules? I wonder if I now have too many controllers, but I doubt is is more than a full home simpit? 

[No1sonuk]

Do you have more than one Leo Bodnar device with the same name?

[Hoirtel]

No, I used the leo config software to change the second to _2. It is similar.