I think I have the same problem,
constantly 40% to 50% nautilus usage, doing nothing.
It seem related to a network share I have mounted. I found its name into
a strace output.
When I realized this, I've tried to access it from nautilus. After this
access, CPU utilization went suddenly down.
Hope this helps!
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nautilus process uses 100% CPU for 30 sec - 2 minutes on computer startup.
https://bugs.launchpad.net/bugs/298663
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