Same issue with our environment. In our case, the previous client was uninstalled via "MSIEXEC /X {product_code}" before Endpoint Agent was installed. The reboot prompt didn't show up until after manually restarting the first time. If it helps I can upload a verbose MSI log. Here's a snippet from the end:
MSI (s) (20:50) [10:01:48:213]: User policy value 'DisableRollback' is 0
MSI (s) (20:50) [10:01:48:213]: Machine policy value 'DisableRollback' is 0
MSI (s) (20:50) [10:01:48:213]: Incrementing counter to disable shutdown. Counter after increment: 0
MSI (s) (20:50) [10:01:48:228]: Note: 1: 1402 2: HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Installer\Rollback\Scripts 3: 2
MSI (s) (20:50) [10:01:48:228]: Note: 1: 2265 2: 3: -2147287035
MSI (s) (20:50) [10:01:48:228]: Note: 1: 1402 2: HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Installer\Rollback\Scripts 3: 2
MSI (s) (20:50) [10:01:48:260]: Decrementing counter to disable shutdown. If counter >= 0, shutdown will be denied. Counter after decrement: -1
MSI (s) (20:50) [10:01:48:260]: Destroying RemoteAPI object.
MSI (s) (20:D0) [10:01:48:260]: Custom Action Manager thread ending.
MSI (c) (28:38) [10:01:48:306]: Decrementing counter to disable shutdown. If counter >= 0, shutdown will be denied. Counter after decrement: -1
MSI (c) (28:38) [10:01:48:306]: MainEngineThread is returning 0
=== Verbose logging stopped: 1/16/2018 10:01:48 ===