Do the bubbles seem more active when the lights are on? Commonly, if these bubbles are rising to the top from the bottom, out of your sand bed this would be denitrification taking place. These bubbles are usually nitrogen, rising to the top and releasing into the atmosphere. This is all normal, seeing how you just "reset" everything back up it is probably going through a mini cycle. If by chance these bubbles are not getting a chance to rise or get trapped underneath your live rock, etc. this can be dangerous, because nitrogen cannot be released. Do a water test and see where your at. I would recommend a powerhead or somekind of jet to help with the release of any bubbles that may be getting trapped. This is also a major factor in why cyano or "red slime" is so harmful, not only does it choke out life, it "carpets" everything trapping in nitrogen and other gasses that need to be released. You may possibly have an outbreak of this during this time, so keep a close eye on it. This is a sign of your biological system at work.
Justin