I have tryed pj64 and dolphin on win2ds and neither of them work with the custom kys how do I fix this.

Im also having the same problem in Cortex Command
*All the custom keys work fine in Windows / Note Pad

They just dont seem to work in this application (If I use the assigned keys on my keyboard, they work fine in-game).
Have tried the game in both full screen / windowed
I will test it out further with some other games

Edit: using Win2DS 0.82, also tried 0.81a same issue.
Edit 2: I think its an issue with this specific game, working fine in other games. Ohwell

I am having the same problem when I use the gamepad on any steam game and on Halo 1 PC.
Does anyone know why this happens or how to fix it???

Well I was playing, or, trying to play MMO dragonica by setting the buttons and using nds as a gamepad, also in game mouse and keys doesn't work but in word, FF, IE and stuff like this it works. Anyone know how to fix it?

I have a similar problem except its with a game called gradchase, help plz

This problem caused by bad KeyPress simulation implementation, so it works only with controls (such as Edit and Memo controls, i.e. known as textfields). Unless there will be a new version with re-implementation of keypress simulation, there is nothing we can do.