There is an annoying bug with custom controller mappings.
I am using the PS3 and XBox 360 controllers on the PC version of MK X. When creating a custom controller preset from the options menu, rather than dynamically changing which buttons correspond with which actions, the game instead keeps the moves and buttons the same but registers the inputs from the controller incorrectly. This behavior is counter-intuitive.
For example: if button "A" corresponds with "back kick" and button "B" with "front punch," and projectile is "down+forward+A", swapping button A and B in custom configuration should change the projectile to "down+forward+B." It does not. Instead, it keeps it as "down+forward+A", but registers button A on the controller as button B. So if I down+forward+B on the controller as instructed on the moves list, I would be hitting the wrong buttons since B on my controller is now being registered as A. This is extremely confusing, and causes the moves list to be useless when using anything besides the default button presets. The moves list needs to dynamically change based on the controller preset like in other games.
We just tested this on Mortal Kombat 9 with the same controllers on the same system, and the behavior in that game works properly without the bug with regards to the button mapping.