There is an option in Mala to re-order the layout, but not sure if that would help in this situation.
Autohotkey cures all though.

Copied from one of my scripts, but originally swiped from here:
http://www.autohotkey.com/community/viewtopic.php?f=2&t=8355&start=30Just change the resolution settings to match your desktop.
#SingleInstance force
SetWorkingDir, C:\Arcade\PC Arcade Ports\Big Buck Hunter\BBH2
Run, C:\Arcade\PC Arcade Ports\Big Buck Hunter\BBH2\BBH2.exe
WinWait, BBHSC
WinWaitClose, BBHSC
exitAPP
LCtrl::~LButton
LAlt::~RButton
c::~ESC
a::~LButton
s::~RButton
]::~ESC
~2 & ~4::
Process, Close, BBH2.exe
cD = 32 ; bits (quality) -
you can change to suit your requirments sW = 1920 ; pixels -
you can change to suit your requirments sH = 1080 ; pixels -
you can change to suit your requirments rR = 60 ; Hz (frequency) -
you can change to suit your requirments ChangeDisplaySettings( cD, sW, sH, rR )
ExitAPP
Return
ChangeDisplaySettings( cD, sW, sH, rR ) {
VarSetCapacity(dM,156,0), NumPut(156,dM,36)
DllCall( "EnumDisplaySettingsA", UInt,0, UInt,-1, UInt,&dM ), NumPut(0x5c0000,dM,40)
NumPut(cD,dM,104), NumPut(sW,dM,108), NumPut(sH,dM,112), NumPut(rR,dM,120)
Return DllCall( "ChangeDisplaySettingsA", UInt,&dM, UInt,0 )
}