If your fans are slower/quieter with the case side off, you may not have
your cooling balanced properly and may have a pressure lock developing in
your system. This can cause overheating due to poor air-flow, no matter how
much air you push in there.
Your fans need to be balanced. What comes in needs to get out. If you have
a lot more coming in than going out, your airflow becomes, um, constipated
:)
It's one of those things folks don't usually think about, and when they
throw another intake fan at the problem they end up making it worse instead
of better.
-Larry