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I have the issue that ubuntu gnome (17) always has the automatic scale factor 2 when using the native resolution (3200x1800). When I change the resolution (to 1920x1080 for example) it scales normally (factor 1). When I look at gsettings get org.gnome.desktop.interface scaling-factor it returns 0. In the gnome tweak tool it says scaling is set to 1. Except for the fact that it is obviously 2. Are there any other options in gnome to set the display scaling or are there hidden mechanisms that scale automatically when choosing a particular resolution?

If I change the scaling factor in the tweak tool to 2 and back to 1, everything scales normally except for the top bar and some notifications. So changing the scaling from 2 to 1 does result in a lower scaling, but does not affect the top bar.

Please help me, this is really annoying.

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A scaling-factor of 0 under org.gnome.desktop.interface means that the scaling factor should be automatically detected, which happens to be 2 in your setup.
The scaling factor setting in gnome-tweak-tool changes a different setting that only affects the scaling of gtk3 windows. To get everything to scale to 1, you need to change the scaling-factor under org.gnome.desktop.interface:

gsettings set org.gnome.desktop.interface scaling-factor 1

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