@Jan De Smet , From your description, it seems the drive mapping is failed with permission issue after we enroll into Intune. if there's any misunderstanding, please let us know.
To clarify our issue, we suggest choose one Hybrid Azure AD join device which is not enrolled into Intune to test to apply the GPP drive map and see if it works.
Meanwhile, I notice the GPP drive map does not run in user securoty context. Could you confirm if it means "Run in logged-on user's security context (user policy option)" is not selected? Based on my research, if this option is not selected, Group Policy processes user preferences using the security context of the SYSTEM account. In this security context, the preference extension is limited to environment variables and system resources available only to the computer. This can cause access denied when it try to access network share. Given the situation, we suggest to select this option to see if it can work
https://learn.microsoft.com/en-us/previous-versions/windows/it-pro/windows-server-2012-r2-and-2012/dn789194(v=ws.11)#run-in-logged-on-users-security-context-user-policy-option
Please try the above suggestions and if there's any update, feel free to let us know.
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