During my last installation of digital experience WebSphere_Portal v8.5 CF12 I ran into problem when running applyCF.bat because one of the server start-up failed. After some investigations I found that the problem occurred because on this system the portal server WebSphere_Portal was registered as a Windows service (via WASService.exe).
The root case of the problem was obviously a delay in the update of the service status on Windows. When applyCF.bat stopped the server via stopServer.bat (or the ConfigEngine equivalent) for a restart immediately after the stop was done applyCF.bat tried to start the server again. As the server however was registered as a service WebSphere tried to start the server via the Windows service interface. But at the time the Windows service was started the status of the service was not yet stopped (still stopping or running - depending on the server performance it seems) hence the start attempt returned an error - resulting applyCF.bat to fail.
Removing the Windows service definition (WASService.exe -remove) caused applyCF.bat to complete successfully.