There is an explanation for this: The baggage system on the eastern part of the building is separate from that in the western part of the building. All SH flights are processed in the western luggage system so if you check in F for a European flight you have a high chance of the bag getting lost. At least that's what I was told the last time I checked in there for AMS - the lady processed me ok but then asked me to take my tagged bag to the fast bag drop in the B area to ensure it travel with me.

Regardless, it sounds like your first guy was a bit short with you perhaps because he wasn't fully informed or bored or tired or had an ingrown toenail or whatever and couldn't be bothered. That wasn't too nice of him was it?