There is nothing wrong with this. Depending on your water's capacity for holding the CO2, your reactor might accumulate some gas and other times be totally empty.
That said, you may be dispensing the gas too fast. Different tank sizes will need different rates. If you slow it down and find that it runs all day and doesn't get the pH to the target level, then it's too slow. But if you are regularly filling the reactor with gas, it's probably too fast.
Do you use tap water? Have you checked your water hardness (GH/KH) in the tank? The site is a bit messed up at the moment, but when it's fixed, they have a nice chart here: http://www.rexgrigg.com/Algae1.html
that lets you determine the CO2 concentration in your tank by the pH of the water and the KH value. You generally want to have a KH around 4 or more. The higher the KH the higher amounts of CO2 can dissolve in the water at a given pH so be careful not to exceed (I think) 40ppm for extended periods of time. At the same time, when using a heavily fertilized, high light tank, low CO2 can lead to algae outbreaks. If you read stuff by Tom Barr at all, his standard response to almost every algae problem is that you're not using enough CO2. And if you don't know your water hardness and adjust it if necessary, I can see where you could have low CO2 and not know it.
So CO2 that reaches the waters surface is lost, but CO2 trapped in your reactor is there until it dissolves which is fine. There is a small possibility that dissolving that extra CO2 into the water once the controller switches off would drive the pH lower and be a problem, but some fluctuation of pH is fine. Most likely you just need to turn the bubble rate down a bit.