Found the problem. I noticed in my logs, I had this error:
php: : The command '/usr/bin/nice -n20 /usr/local/bin/rrdtool update /var/db/rrd/wan-queues.rrd -t :wan:qACK:qDefault:qP2P:qVoIP:qGames:qOthersHigh:qOthersLow N:U:U:U:U:U:U:U:U' returned exit code '1', the output was 'ERROR: unknown DS name '''
Removed the traffic shaper, ran rm /var/db/rrd/queue and re-enabled the traffic shaper and now everything is grand. As expected, I've lost all queue data, but the totals are there and now make sense. As a good side effect, my status -> queues also now make sense (before they did not show data that made sense).
The problem does come back quickly though.