Have had a similar baffling experience, being the simpleton that I am now means I always go to the staff counter, and if directed elsewhere its only a 15 metre walk back out to the J bag drop off, not the end of the world IMHO.
Staff travel is a privilege (necessity for me) and one wants to abide by the rules, but its next to impossible at times when the rules change on a daily (hourly) basis
The most frustrating thing about it all is, often, the staff on the counters don't know either..so we just muddle through as colleagues
