I just signed up with my Github account, but the signup form filled in my secondary email (which happened to be no longer accurate). However, I couldn’t change it anymore, so first created my account and then changed it in this Discourse forum account settings afterwards instead.
PS I don’t need help with this - I entered the forum, just reporting 
PS2 Originally posted here: Signup via Github doesn't use primary email - Site Feedback - Let's Encrypt Community Support
I confirm this. Yesterday I registered to https://discuss.gradle.org (2.0.0.beta3) using my github account. Non-primary email was chosen (it used to be primary a year ago).
It could be related to my last commit in GitHub authenticator. I will check and confirm here.
It is fixed now per below commit
https://github.com/discourse/discourse/commit/c5d26992d48f686e6623fd78a3a065890d1fe07c
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