In gnome, it seems like if you have GIT_ASKPASS / SSH_ASKPASS env variables set then git will automatically use that to query for user password.
This can be somewhat irritating. To work around this issue, try running:
unset SSH_ASKPASS
unset GIT_ASKPASS
If you only want to disable the query for password in git. You can also set the core.askpass settings:
git config --global core.askpass ""