There is a UserClassGroupID setting in the [UserSettings] block of site.ini
# Which class group that has user classes, controls which classes
# is shown on the user navigation part. If empty all classes are used.
UserClassGroupID=2
That is weird how you have Content and Media classes showing. You might also want to double-check the [NodeSettings] settings in content.ini:
[NodeSettings]
# The node ID of the normal content tree
RootNode=2
# The node ID of the user tree
UserRootNode=5
# The node ID for the media tree
MediaRootNode=43
# The node ID for the setup tree
SetupRootNode=48
# The node ID for the design tree
DesignRootNode=58
