Hmm, I'm not sure but I think XF86Config-4 needs no Modelines anymore. So it should work if you just add the Mode "1280x1024" to the "Screen"-Section". Of course you have to make sure, that your monitor is described right. Here's an example:
Section "Monitor"
Identifier "AOC Spectrum 7GLR"
HorizSync 30-96
VertRefresh 60-100
Option "DPMS"
EndSection

Section "Screen"
Identifier "Default Screen"
Device "Geforce4 Ti 4200"
Monitor "AOC Spectrum 7GLR"
DefaultDepth 24
SubSection "Display"
Depth 1
Modes "1280x1024" "1024x768" "640x480"
EndSubSection
SubSection "Display"
Depth 4
Modes "1280x1024" "1024x768" "640x480"
EndSubSection
SubSection "Display"
Depth 8
Modes "1280x1024" "1024x768" "640x480"
EndSubSection
SubSection "Display"
Depth 15
Modes "1280x1024" "1024x768" "640x480"
EndSubSection
SubSection "Display"
Depth 16
Modes "1280x1024" "1024x768" "640x480"
EndSubSection
SubSection "Display"
Depth 24
Modes "1280x1024" "1024x768" "640x480"
EndSubSection
EndSection