It's normal for a skimmer to put out copious amounts of micro bubbles while it's breaking in. There's no way that skimmer is broken in yet if it's only been running intermittently the last five weeks. As to it performing well when it's was running earlier, most likely it's because when you add live rock, there is always natural die off on the rock from the transition, or if you put in live sand, same thing. The skimmer most likely was pushing out the die off. Now that the rock and sand die off has started stabilizing, the skimmer is slowing down and idling until it develops a more consistent slime coat while it breaks in.
Hands in tank, frag glue, new equipment, filter socks, certain foods, etc.., etc.. can all contribute to knocking down foam heads on skimmers and generate micros.