gpg spawns a background process to update the trustdb at some very
regular time.  I suspect this may be what's going on.  I noticed this
when using gpg through mutt in that mutt would wait a very long time
once in a while.  I wonder if evolution is killing it?  Robert, does
adding this to your .gnupg/options file make it go away?

no-auto-check-trustdb

With this option, you need to run the trust checker once in a while, or
gpg gets mad.  I run this once a day from cron:

37 5 * * * gpg --check-trustdb 2>&1 | egrep -v '(depth: | needed,|next
trustdb check)'

-- 
evolution causes gpg stale locks
https://bugs.launchpad.net/bugs/42199
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