This is something I too have noticed and have been actively investigating. The path is (should be) saved in the registry under start > run >regedit
My Computer\HKEY_LOCAL_MACHINE\SOFTWARE\QlikTech\QlikViewServer\Settings 7
value is DocumentDirectory if for some reason when the qvs starts up it can not access the current directory it will go to the default directory in order for the service to start. I hope this provides a "sort of" explaination as to what is happening. I know it doesn't exactly resolve the issue.
Can you provide some more information as to the path of your document directory, i.e. NAS, Shared Drive, SAN, etc?