Theoretically, an aquarium that has had fish in for 6 months should be cycled. However, because the filter was changed about 3 weeks ago, this could be contributing to the problem. I know some filter material was transferred from an established filter into the new filter and that should help, however it might not have settled in.
The new filter does a pretty good turnover (1000 litres per hour). You could try reducing the flow a bit and see if that helps.
I think your tank is one of those funny ones that takes 6 months to establish and there is something that is slowing it down. It happens occasionally with people having ammonia and nitrite readings for 6 months after a tank was set up. The tank normally settles down.
Do you have anything in the substrate, eg a plant soil or something similar?
That might be leaching stuff into the water.