Company Portal not installed (device based install with pre provisioning deployment)

I hope this thread is still valid, i am also observing intermittent behavior with company portal deployed in ESP(system context). Company Portal is getting installed for system account even in Intune portal it shows as success but after a user is logged in, the apps goes missing. When we switch user the app is available. . We were able to fix by deploying user context company portal app to the failed user machines