In my situation problem is different: ethernet packets and rate are bigger than total_queue packets and rate (see last image) and so I would know why.
Oh, sorry, I thought it is contrariwise.
I had some strange traffic on my WAN port once. It was nearly constant 2 Mbps and was there also when there was no traffic on LAN. So there was more traffic on WAN interface than on LAN interface (and Queues). What about you? You have smaller traffic on Queues than on WAN interface. But is a traffic on LAN interface also smaller than on WAN interface? If it is so, check WAN connections. I've had disconnected my LAN (besides me), started tool "torch" and found some other Mikrotik on WAN interface that was badly configured and was still sending me data - it was other customer of my internet provider.