I had this issue with WebStorm recently (February/2018) and none of the (then) previous solutions worked for me. After spending some hours on troubleshooting and researching, I installed the 2018 EAP version and now it works!
A new issue reported on December/2017 on IntelliJ Idea > VCS/Git subsystem which was fixed in build 181.2445 (or any latest build after 31/Jan/2018).
See also the post Update-ssh-key-to-use-new-passphrase