The only time I know of that terraforming installations stop doing their work is when they reach target atmosphere density. Since I don't know how well you know the game, I'll just go step by step.
When you start terraforming you need to specify what kind of gas you want to change. Be default the terraformers substract gas from the atmosphere, unless "add gas to the atmosphere" (or something similar) box is checked. Then you need to specify target atmosphere density. Then you may need to press "save atm" button. I'm not really sure, I think terraforming may work without clicking it.
Once the terraformers substracted all the gas specified, or added the amount specified, the terraforming "resets" itself - the window showing gas being added/substracted will change to "terraforming inactive". In this case, you need to repeat the whole prcedure.