It was hard for me to discover it at first, but in my MK3 the UP-pad is triggered forever (the character is always jumping - obviously).

Just to check, it happens without any joysticks plugged, just the keyboard, and it does not occur in the MK1 & 2.

Someone had a similar issue?

I have this exact same issue and no solution yet. I will post here if I find one.

Problem solved.

All you need to do is download the Xpadder or any other similar program and config your controller.
After that, in the Mortal Kombat 3 folder, open the file "dosboxMortalKombat3".
In the "Joystick" Section disable the Controller Emulation. Look for "joysticktype=auto" and change for "joysticktype=none".
Start the game and config your controller pressing "ESC" en the Buttons Config Menu.
Now your controls in game will work perfectly.

Thanks, it really worked.

I have to add a tip here for someone that could have the same problem and pops up here in this thread too, that open up the file "dosboxMortalKombat3" in notepad could be awful, so use notepad++ insted.

character jumps backwards all the time and even in the menu screen I can't control anything, as if someone else pushes the keys randomly. Xpadder doesn't help while every version that I found wasn't compatible with Win 10. Is there any other solution for this?

i set the controller like the screen say to do. but the game move solo without any input. i try to play with keyboard i can move the character now but the game take action in solo in menù . when i try to select a charatcer i have only 1 sec for do it and the game in solo accept and continue. same for choose the difficulty tower, is totally random. so i need to know ho i can fix the controller for use it like actually the keyboard , and fix the game accept and move solo in menù