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My VGA monitor is recognized by X11 and best resolution is chosen, which is correct with product specification. This resolution sometimes does not always work in practice (frequency out of range error briefly appears). This may be hardware problem, I'm looking for a workaround ideally targeting that particular malfunctioning device.

VGA1 connected primary 1280x1024+0+0 ...
   1280x1024     75.02*   60.02

So far I know how to fix it temporarily:

xrandr -d :0 --output VGA1 --mode 1280x1024 -r 60.02

This is far from ideal, because I'm blindly forcing resolution for all monitors. Plus, I'm not sure if /etc/X11/xinit/xinitrc is good place for it.

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Reset to default
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The command should be:

xrandr --output VGA1 --mode 1280x1024 -r 60.02

There is no need to specify the display if you are already specifying the monitor.Also, you really want to specify the resolution and refresh rate for the monitor, not for the screen, which is the origin of your problems...

because I'm blindly forcing resolution for all monitors

Also, xrandr is not part of X11, so you can put that ommand wherever you want, in /etc/rc.local, in a crontab file to be executed at boot,

 @reboot /path/to/xecutable/script/containing/xrandr
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