Duplicate loads isn't normal behavior, so there's something wrong. Either your files are being delivered twice, or arsload is processing them twice.
You'll probably want to upgrade to v9.0.0.7, since there are a lot of bug fixes, and this one sounds like it might be similar:
PI19747 - Arsload shows msg 87 while zero rows inserted in the DB
LoadIDs should be unique for every load.
-JD.