I cannot tell you how much I hate check-in at BER this year.
Every single time I fly from there - it's either opening late, or there is no priority queue, or the people spend 30 minutes chatting when they should be checking in or the incorrect tag being attached (don't ask me how it happened). Another issue is that the screens tell you check-in is open at T-3h but the people actually on turn up at T-2h or sometimes T-1.5h.
I would log a complaint/customer service form about this. I would be interested to see their response.
For anyone departing BER I would strongly suggest you check the tag they put on your bag, and if it's fragile, make sure it is correctly indicated so and don't turn up at T-3h despite the screens telling you it's open (if not HBO).