I have reached out to ME support on this, but I am getting nowhere, so I figured I would reach out to the community for help. 

Situation:

We are in a hybrid environment with on-prem AD and online exchange. When creating new user accounts, we have two alias email addresses added. When doing this manually in exchange online, the M365 mailbox user is generated correctly. 

Problem:

When creating the user in ADManager Plus, the primary email gets set as an alias, and one of the alias addresses gets set as the primary email. According to ME support, our user creation template is set correctly. We have proxy addresses set in custom attributes. 

Has anyone experienced this before where one of the proxy (alias) email addresses is getting set as primary instead of an alias? The screenshot below is from the 365 admin portal.