The problem doesn't have anything to do with GSX.
As explained so many times on the forum, what you are probably assuming to be the "GSX menu", it's NOT the GSX menu. It's the Simconnect menu, which is handled entirely by the sim, used by all 3rd party applications with a menu, and none of them has any control over it, or how the menu will respond to the keyboard.
The issue with the numpad problem, which has been discussed so many times on this forum, and on every other flight simulation forum (since it's doesn't affect just GSX, but each and every addon with a menu), it's a very well known P3D 4.2 bug, which result in the keyboard not being read correctly when ANY application with a menu is being used.
LM is fully aware of this P3D 4.2 bug, and will be fixed in the next update of the sim.