Had the same thing on FRA-LCY last month. Slightly annoying as I spent quite some time getting all the documents into Verifly, got the green tick, and then couldn't check in online. The queue was about an hour for check in - very much the way the OP described. The only difference was that FRA strictly patrolled the Club check in line (made no difference as both lines were roughly the same length).

Given the JAL lounge only did bottled water to take away (no eating/drinking in the lounge) I didn't feel massively cheated.