What type of skimmer do you have on what size of tank? I had a hang-on skimmer with my 20 gallon before I took the tank down, and whenever I added water or other addatives there were some bubbles. The instruction book said that this was because of the amount of air added was slightly off because of the slight water chemistry change. You might try adjusting the air valve to see if you can get it better. Also, how long have you had it running? It took my skimmer a few days to stop over-bubbling when I first set it up. Just some ideas, hope they help.