for future reference, vaccuming sand is not a good thing because not only does it often cause a sandstorm, but it also takes out bacteria and creatures, also taking away the point of live sand.
but this is my guess, you left the skimmer still for 2 days. that also leaves the water still in it. The water will become stagnant and basicaly turn bad.
i agree, check for an amonia spike, that might be the cause of one.