The chiller comes on maybe 5-6 times a day, but with the 90 degree turns from the accessory port to the chiller and back, there is quite a reduction in flow.
Also, Eheim 5000 has a max flow rate of 1320 gph not 5000.
When I feed a little heavy, I see changes within the tank within 2-3 days. The RSM 250 has it's limitations based on the current stock setup, so first thing I would do is look at the amount your feeding.
Also try Brightwell Aquatics MicroBacter7...
I think AIO (All In One) tanks are great for the beginner. I had mine for 15 months, but once you gain experience, you see the AIO systems have limits. I think an RSM 130/250 are great starter tanks, see if you really enjoy the hobby and learn as you go. The the keys is being patient!