I don't know if this is a clue but it looked very strange:

Some time ago I noticed that every time I checked processes with gnome
system monitor ntop would use a lot of cpu (50-100%). When I killed ntop
system monitor would be killed too! It happened consistently. Eventually
I removed ntop in synaptics. After that system monitor would use 80-90%
cpu and it took several seconds to resize its window. I then reinstalled
ntop and now it runs normal 5-20% cpu, I can kill ntop without side
effect.

Still ntop is apparently started automatically by system monitor
(apparenatly also other *top utilities like atop)

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Excessive CPU usage by Gnome System Monitor 
https://bugs.launchpad.net/bugs/93847
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