If your Microsoft Project file is in manual scheduling mode and you did not select this option, it could be because:
The previous synchronization with Project Management failed. During synchronization, in Project Management-controlled mode or shared control mode, the scheduling mode is set to manual and then returned to automatic once the synchronization completes. If the synchronization did not complete, the scheduling mode may have been left in manual.
You opened a project that was in manual mode and then created the Microsoft Project file resulting in the project inheriting the manual mode setting as a default.