With a cya of 60, a chlorine reading of 2 is too low. You need to be keeping your cl between 5-10 all the time. And, shocking to about 15. See the chart at the following link. This very well could be a part of your problem. Shock your pool up to 15 using bleach and try and keep it there without letting it yo-yo up and down. If you can, test 3x a day and each time bring your shock level back up to 15. You never did say what type of granular shock you are using, but whatever it is, quit using it. Stick with just bleach. Run your pump 24/7.
http://www.poolforum.com/pf2/showthread.php?t=365
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