Good news we have found what seems to be the source of this issue.
Details and temporary fix at
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=773130
Leaving this issue open as we don't yet know if the bug is cause by
nautilus or gvfs or gvfsd-metadata or all of the above
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Every time this bug occurs the package gnome-shell uses 25 to 75% of
the CPU. So gnome-shell seems to be somehow related to this issue.
Steps to reproduce
1. Follow steps to reproduce at
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=767276#5
2. When the Loading... icon appears at the bottom
Related issue at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=523048
It seems gnome assistive technologies is involved in that issue
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