This issue is also observed on systems without inSync Client installed. A patch released by Microsoft (KB3197868) seems to be causing this issue. Due to the patch, processes running on a device are continuously monitored, causing a delayed shutdown. Stopping inSync services or disabling monitoring is one workaround but it is not recommended. Microsoft has acknowledged the presence of this issue and has also released a fix (KB2461484).
For a detailed explanation, workaround & fix details, please refer to the following KB: