You're better off just having the lights on for a shorter time during the day. I'm assuming you have a timer. having the lights go off for increments during the day is totally not natural. The closer the fish are to their natural environment, the healthier and happier they will be. I don't know of an environment fish live in that would have periods of darkness during the day. The algae should be physically removed through gravel cleaning or taking out rocks and scrubbing off the algae. additionally, don't use any products that contain phosphates as this will give the algae a boost in growth. If you thnk you may have high phosphate levels, try using phosguard, or another phosphate remover. Phosguard is made by seachem which IMHO is the best chemical manufacturer for freshwater.