What kind of CO2 are you running? Can you describe your system, especially if it is a DIY system?
How are you diffusing the CO2?
How long has it been running?
Are you using 4dKH solution in the drop checker?
Do you have a KH test kit, and a pH test kit? If so, what are the values of each?
Are you disturbing the surface of the water with filtration or a powerhead?
What kind of filtration are you using?
1 bubble every 2 seconds sounds like waaaay to slow of a rate for that size tank, regardless of the answers to the above questions... I would think in a 40gal tank, you should be aiming for more like 1-2 bubbles per second depending on your method of filtration. I run a 12 gal tank at 1bps using a glass/ceramic diffuser.