Ok, since you had two systems one working and one not the first idea was to find what was different, simply having a different desktop would normally be considered to have no effect.

But in the absence of any other differences I guess its Gnome's fault, maybe its causing GTK to do something in the background, like enumerate filesystem contents in case you open the file chooser or something similar.

Did you check for anything else using CPU in the Gnome case?

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