I have had this issue since June and have also complained to customer relations several times. The most recent time they told me it was because I was booking through a travel agent (even though one flight was booked through the explat desk) and referred me to web services. I got frustrated enough to file a DOT complaint, which is currently pending.
I do not believe this is a bug with kiosk because when I go to the counter, they report the same thing as the kiosk (bag allowance shows 2 bags). I've found the fastest course of action if the agent won't waive the fee is to ask them to call RSD.
I had one trip where my baggage allowance was 3 on the outbound but only 2 on the return. I think (but don't know for sure) this only happens when I do a same day flight change or there is a change due to irrops. I know that was the case with all but one trip where I experienced this, and can't recall if it happened on that one trip.
Has anyone seen a connection with this and SDFC or a flight change for irrops?