take a look at the settings in [RelationAssignmentSettings] in content.ini
You may store them in a correct node-tree, and then they will inherit the correct section. If not, these files remain "nodeless" and also without a section assigned (unless you give them a correct node placement in the edit screen). Or are you using the objectrelationlist datatype?
[RelationAssignmentSettings]
# Default assignment for new related objects, possible values are
# - A Node ID - Place all new objects under this node
# - root - The root of the tree
# - users - The root of the user tree
# - none - Do not place anywhere, the user must then fix the assignment before publishing
# Multiple assignments are separated with commas.
DefaultAssignment=2
# Overrides for specific classes.
#
# Each entry is a list of comma separated values, the first is the match
# and the second is the assignment (see above for values)
#
# Classes are either specified with identifier, ID or group_ID
# The items are searched in order so the first to match will be used,
# this means that class IDs should come before class group IDs.
ClassSpecificAssignment[]
ClassSpecificAssignment[]=user,user_group;users
ClassSpecificAssignment[]=image;2876
ClassSpecificAssignment[]=file;2877
