Thanks for the post and confirmation things are now working. The scenario you describe is generally caused if the proxyAddresses attribute for an Active Directory user has missing or incorrect SMTP information. When the user is provisioned to Office 365 and a default SMTP value is not present in the proxyAddresses attribute, Office 365 will reverse sync and populate this attribute in Active Directory using the default domain selection configured in the Office 365 portal. Since the default domain is generally one that contains "onmicrosoft.com", this is the same information Office 365 will use to populate and is clearly not a desired value.
You would generally want to populate the proxyAddresses attribute with a valid primary SMTP value and any secondary values for additional addresses. Here is an example of what the configuration should look like when viewing user properties in ADUC - note the use of capital "SMTP" to designate the primary address:
Would you be able to confirm if this was indeed the root cause of your issue in case other folks encounter a similar experience? We appreciate any details you may be able to offer.
Glad things are working for you and thanks for using Centrify!
-Tony