Considering the above, yes it a simple way to check if it comes from your keyboard or if the problem is elsewhere.
You don't delete anything. You save all your settings:
file/controller manager/ and at the very bottom you can import/export. Export all your settings (check where it is saved).
Now once it is saved, in the controller manager, just under "device set up", you have "device", select one, push the edit button (just to the right of the "add" button") it open a menu and click delete (repeat for each one of your controller).
Then, recreate a new controller keyboard: click on "add", select generic keyboard, check it is set on device target "focus", check that all "modifier state"(s) are set to 0. The in-port should be keyboard (use your main keyboard not the usb one at the time being).
Add in 4 functions that would be: transport/Play -pause/ learn button A/ no modifiers conditions/ type of controller Button/ interaction mode Toggle/ Assignment deck A. Note that would be good to use 'common' buttons on your keyboard, no shortcuts or anyhting fancy, try with the num-pads.
Repeat the above for buttons B,C and D (and assignate to decks B,C and D)
Click one again on learn so it's no yellow anymore, recheck you didn't use by mistake the same button (oh yes it happens!), check the assignment of each deck. Now close the controller manager.
Try to have 4 decks playing at once if triggered by mouse, if it's ok, stop them and now trigger the play/pause with each deck, then two, then three, then all at once (change combinations). What happens, is it the same decks that are in fault, what about if you change the 'deck focus' directly on Traktor, does that change the behaviour?
I know it sounds simple but at least from a 'naked' set up, if that doesn't work, we can now pass easily to another step, but we'll know and won't assume your mappings and buttons aren't in conflict with 'something'.
Now you import back your settings after deleting our try at a new generic keyboard.
All the above won't take much time so it's worth trying don't you think?
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