Almost certainly, due to low pH. This may be pool wide, or you may have been running chlorine tabs (acid!) in the skimmer, and also using a timer, which results in a low pH / high chlorine 'hot shot' hitting the heater, ever time the pump kicks on, after being off for a few hours.
Raise your pH with borax to above 7.4; do NOT use skimmer tabs IF you use a timer.
To fix the stains, you'll need a K2006 test kit (see link to test kit page in blue signature block).
Try to avoid 'shocking' the pool, which can result in ALL the copper remaining in your pool water suddenly taking up residence as even more stains. Reading this thread will explain more: http://www.poolforum.com/pf2/showthr...acid-treatment
BUT, don't start on that treatment process, till you've gotten a handle on testing and managing basic pool chemistry YOURSELF.
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