I never seemed to have a problem with this setup, but now am wondering
if its not such a great idea. Should I instead put the light on for 12
hours continuously? Say from 11 am to 11 pm ? Is there a difference
for the plants in processing CO2 and O2 ?

The whole concept of keeping the tropical plants at home is to bring the
"nature" to your living room. Why are we having powerful lights? -
Simulating sun light.

Initially I had 2x6 lighting with a gap of 4 hours. but now I have 1x12 and
I see lot of changes. Plants are growing fast. Their nutrient intake is
more. In 1x12, my plants continuously pearl for about 11+ hours. In 2x6,
plants will go to sleep more in the "off" period.

This is my $0.02.

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Thank You

Dominic
http://www.dlink.org/aqua