Managed configuration not getting pushed onto some devices in work profile

My team uses AMA API to managed devices. As part creation of enrollment token we push some applications and managed configuration to those applications as part of the policy. But we are noticing that this is not very reliable. We have many user stories where the app gets installed but the managed configuration is missing. This doesn't happen on all devices but the occurrence of this has been increasing. Is there any known issue or SLA on how long it takes for the managed configuration to be pushed? 
We have an Application that is set as Required for Setupin the policy. This Application has managed configuration setup, which is required for App registration. This is missing by the time app launches and app registration fails and consequently the work profile provisioning fails.