After plugging the second monitor, I could not find the correct resolution in nvidia-settings and it was impossible to do it manually. After having to solve this problem for the second time, I post it here so to remember.

1. Look at nvidia-settings for the name of the monitors (In my case DFP-0 and DFP-7).
2. nvidia-settings -a CurrentMetaMode="DFP-0: 1920x1080+0+0, DFP-7: 1280x1024+1920+0 { ViewPortIn=1280x1024, ViewPortOut=1280x1024 }"

Where DFP-7 is the problematic monitor and 1280x1024 is the correct resolution.

I hope this is helpful for someone else.