I had this exact same problem 2 times last summer with my cover. I assumed that my cover itself was "contaminated" with with live algae after being off for a while, so that even though the pool itself was clean, it started to grow into the pool. And the pool gets much warmer with solar cover. (Your cover was new, so my theory doesn't seem to work so well.)

This year, I'm going to try to rinse off the cover really well before putting it on. I'll also not use the cover if the water gets to the high 80's.