Comment 14 for bug 246364

It is a enigmail-issue. Invalidating the seahorse task and reopening the enigmail one. Enigmail performs two separate actions, see upstream's comment:

"From the enigmail ouput pasted in the enigmail forum, enigmail is performing
two different operations:

enigmail> /usr/bin/gpg --charset utf8 --batch --no-tty --status-fd 2 -t --clearsign -u 0xA81E15E0 --use-agent
enigmail> /usr/bin/gpg --charset utf8 --batch --no-tty --status-fd 2 --digest-algo sha1 -s -b -a -t -u 0xA81E15E0 --use-agent

If your option is set to have the agent not remember your passphrase, you will
be asked twice for it because it's not being cached from request to request.
If changing the caching option from never to expires after a period of time or
always fixes this behavior, then everything is operating as designed. If
that's not the case, please reopen this bug. "