I don't believe there is a global parameter to store files in the database or filesystem. Currently it is application dependent.
There are two ways I can see to fix this.
1) Add a parameter to acs-content-repository for a default setting.
2) For dotlrn-fs have subgroups use the parameter of the file-storage instance of the main group.
In addition the latest verson of file-storage in CVS on the oacs-5-1 branch has been changed to storing files in the filesystem by default.
