I'm having a similar issue with GitHub authorisation in Atom Beta (18).
I have been using the GitHub desktop app together with Atom for several months successfully. I branch, I sync (push and pull), I commit, I do pull requests. I've also been using the MergeConflicts package without problems.
I was really looking forward to switching to Atom Beta to do all my GitHub tasks. I can stage and commit without problem. But every time I push or pull, I have to enter my username and password. And there is nothing in the GitHub (preview) pane. Even when I switch branches to a branch which has a current pull request, it is not picked up by the GitHub tab. I have to manually enter the GitHub URL.
How can I get Atom Beta to a) pick up and b) retain my GitHub username and password? I would be very grateful for your help with this.