Dual valve CO2 issue

I would personally look into the check valve first, my reasoning for that being is that IMO it's the most likely piece of equipment to fail. Try swapping the check valves between the two lines and see if the problem switches sides. If you don't mind spending the money on a new check valve buy a replacement and swap out the old one, that way you only have to take apart one line instead of both.

Check valves aren't meant to last forever and do require checking/replacing. That's why I opted to run inline check valves close to my tanks so I can easily inspect them while doing my weekly maintenance. Although having a bubble counter set up like you do does prevent you from removing the check valve from between the needle valve and bubble counter.

I had a similar problem on one of my co2 set ups and it turned out to be the check valve sticking. If that isn't the problem I would check the needle valve next. Hopefully it won't come to that. Good luck.

If it is not the problem of the check valve, water maybe leak into the needle valve.

I also have check valves inline between the reactor and bubble counter.

Run the system after removing the tube from the Bubble counter, so that you can narrow down where the problem is.