Depending on how you are calling the SSIS package, you may also want to check the login for the Agent Job. I believe that any jobs scheduled through SQL...

Will there be other deletes on SUB that you will want replicated to MAIN? If not you can adjust your articles to not replicated delete commands.

What type of publication do you have set up? Transactional or Snapshot?

One thing that may help is to generate scripts to see what may be different with the subscriptions.

I know this is an old post but I also ran into the questions while working with replication and figured I would post my findings in order to help anyone...