I think you are dealing with mustard algae. I had a wake up call with this stuff in June. We noticed it towards the end of last year and thought nothing of it until it consumed our pool this year. Our daily regimen was to increase the chlorine to shock level (we intentionally overshot this regularly) in the morning and evening, vacuum, change cartridges (we have a cartridge filter and an extra set of cartridges) and run the filter 24/7. We also used skimmer socks to grab what they could. At the worst, it took nearly 2 weeks to be rid of it. Now, we seem to get it whenever we use the solar cover or if I haven't brushed the pool in a while. If caught early, we just shock, brush and let the filter take care of it and it's typically gone the next day.

My fight - http://www.poolforum.com/pf2/showthread.php?t=3287