Depois de semanas e semanas brincando, finalmente consegui descobrir meu problema! Foi, de fato, o monitor.
Eu segui o guia aqui e editei manualmente o arquivo xorg.conf, e agora tudo funciona perfeitamente!
Adicionando o conteúdo aqui apenas para o caso de os fóruns serem arquivados:
# This section defines the Catleap (HiRes) monitor.
# I just left this section completely the same as in the example
#
Section "Monitor"
Identifier "Monitor0"
VendorName "Shimian"
ModelName "QHD270"
HorizSync 88.8
VertRefresh 59.5
Option "DPMS"
Modeline "2560x1440" 241.50 2560 2608 2640 2720 1440 1443 1448 1481 +hsync -vsync
DisplaySize 597 336
EndSection
#
# This section defines the video card, I didn't change anything here either
#
Section "Device"
Identifier "Device0"
Driver "nvidia"
VendorName "NVIDIA Corporation"
BoardName "GeForce GTX 460"
EndSection
# This is the section I changed
#
# The BIGGEST issue I had, was figuring out what was on DFP-0, DFP-1 and DFP-2 (which are the dvi/hdmi outputs)
# In MY system, DFP-0 is the "primary" DVI output
# and DFP-1 is the mini-HDMI output
# and DFP-2 is the 2ndary DVI output
# So I want my Catleap on DVI-0 and the Asus twinview monitor on the DFP-2 (so I had to change my cables)
#
Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor "Monitor0"
DefaultDepth 24
Option "NoLogo" "True"
Option "TwinView" "1"
# Leave this as DFP-0, which is where the Catleap(hires) monitor is plugged into.
# This (I believe) tells the system what the "primary" display is in the twin view
Option "TwinViewXineramaInfoOrder" "DFP-0"
Option "UseEDID" "False"
Option "UseEDIDDPI" "False"
Option "UseEDIDFreqs" "False"
Option "ExactModeTimingsDVI" "True"
# This is the only other line I had to change from the example
# DFP-0: 2560x1440_60 +0 +0 <--- This line is the "primary" display on DFP-0 (the Catleap HiRes)
# DFP-2: 1920x1080 +2560 +0 <--- This was for the 2nd monitor, resolution and offset.
# Don't forget the comma between the two monitors
Option "metamodes" "DFP-0: 2560x1440_60 +0 +0, DFP-2: 1920x1080 +2560+0"
SubSection "Display"
Depth 24
EndSubSection
EndSection
Section "ServerLayout"
Identifier "Layout0"
Screen 0 "Screen0" 0 0
Option "Xinerama" "0"
EndSection