Over the last week, could not figure out where these "flakes" were coming from, thought it was from one of the trees. They kept getting sucked into the filter, past the skimmer basket, and plugging the sand filter.
Lo and behold, it was my old clear solar cover starting to disintegrate and the bottom of the little bubbles were falling of it! Floating on top the water, they were sucked into the filter system, and plugged it pretty good. I was trying to get one more season out of it, but its really bad now, so off to the store today to get a new one.
So just a word of warning to keep an eye on your old covers, replace them.