Gunzip is pretty cheap, so I wouldn't worry about this for your traffic levels.
If this is a Varnish 3.0 server, you can safely remove the Accept-Encoding scrubbing in vcl_recv. This will be done behind the scenes by Varnish itself.
As for a root cause, my guess is that this is your service monitoring probe that forgets to set Accept-Encoding: gzip
. Your probe URL (front page/favicon/probe.txt) is stored gzip-ed inside Varnish, and these repeated checks are skewing your gzip rate.