Can you provide more information about your aquarium? Lighting, substrate, tank size, fertilizing, CO2, etc.? That might suggest some problem to some of us.
The CO2 content in the tank, after a night of no Co2, isn't necessarily 3 ppm, but could be 4-5 ppm, which would mean you have a lot more than you think. I like the idea of isolating a cup full of water over night or longer better.So just before the co2 is switched off I have a ph around 6.5 and next day in the morning, just before the lights turn on I have Ph of 7.0
Does it mean that I have just 15ppm so I should increase CO2 level to go near to 30 ppm?
I realised also that when the kh is 3.5-4 the ph difference is 0.5
However as I am getting close to the water change my kh increase until 6 due to the seiryu stone, then the difference is just 0.2 but I put same co2 in the water...