I got hit by the very same bug, while using the yubikey with ssh: Package: pinentry-gnome3 Version: 0.9.7-1 Debian Release: stretch/sid Architecture: amd64 (x86_64)
Probably interesting: - Neither pinentry for the yubi-key, nor ask-pass for a classic ssh key with passphrase show up, so maybe this bug needs to be shifted to gnome-keyring? Not sure, what's the real issue here. - If I decrypt a message in thunderbird first, a pinentry shows up and afterwards the cached pin is used for the ssh connection as well. Bjørn