Hi,
Thank you for posting in Microsoft Q&A forum.
Are you set the user portal to Company Portal in Software Center client setting? If yes, this may be expected behavior. This setting makes sure that notifications from Configuration Manager and Intune both launch the Company Portal.
Company Portal version 11.0.8980.0 or later shows Configuration Manager-deployed applications for all co-managed clients that use it. Configuration Manager version 2006 is the prerequisite because it adds the client setting to control notifications.
Refer to the official articles:
Thanks for your time. Have a nice day!
Best regards,
Simon
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