Im not sure what exactly causing your problem , but this may help you troubleshoot .
-when you press a button there is 3 stage , PressDown , Hold and Release. make sure your keys register the release. so check your drivers and make sure your button act as normal button and not toggle outside the game first.
-sometime game is not listening to your input , like when you open pause menu , in my case modifier that was toggled on would register as off after closing the menu and required toggle off and then on again to work , this is opposite of your problem but something to think about.
-Working with modifier can cause a lot of conflict if not setup properly , you need to spend extra time to check everything and make sure that is not a case .(this is most likely your case)
-None Plane specific master Category in adjust controls like General or UI can potentially cause conflict with your Plane specific category .
-Since you say the modifier is working as expected with other actions =>
then Test : after you press THUMB key without MOD and you got ptt 2 as a result , try pressing another action that does use same modifier (MOD) without pressing the MOD to see if it is executing , If not( As Expected ) Try pressing your THUMB key again to see if ptt 2 still execute , If so try to use different key as modifier and see if you have same problem still .
=> if Yes , Run integrity check on your game file make sure there is no corruption .
=> if No , Then your issue is either from your hardware or its driver .
It is not easy to pinpoint your problem without knowing how you setup your modifiers , your keybinding , your hardware and your software setup outside of the game.