This bug has been discussed so many times already on all forums and yes, GSX doesn't have anything to do with it and cannot do anything to prevent it.
It's a known P3D bug that has been introduced with 4.2, and affects *ALL* application with a menu, including the samples from the SDK provided by LM, and it's actually 4 bugs at the same time:
1) If you (or another addon) press/send a numeric key before opening the menu, that key will be sent to it automatically, auto-selecting the menu.
2) If you press a number that is higher than the number of available menu options, the key will be sent to the app just the same (it wasn't like that before), confusing the application that only expected options to be in a certain range
3) The numeric key you pressed will be sent to the sim as well so, for example, if you are in slew mode and select option 9 from an application with a menu, the 9 will be sent to the sim, so the plane will start to pitch up, because that's assigned to pitch up in Slew mode. It shouldn't work like that.
4) Opening a 3rd party application that has a menu, prevents to control the right rudder with the keyboard.
All 4 are fully acknowledged P3D 4.2 specific bugs, they affect each and every 3rd party application with a menu, none of them is a GSX problem or something that GSX can fix for itself, LM is aware of them, and the only thing to do is to wait for LM to came up with a fix.