What kind of filter is it (i.e. canister with spraybar or HOB)? Do you have any control of the direction of the outtake? What tells you your fish are having a problem with it? What kind of fish do you have?
We need more information.
Generally having the outtake pointing upwards near the water surface will reduce flow within the tank because the water being pumped back into the tank will mainly be agitating the surface (and improving oxygenation). I have a 110 gallon tank with about 1800 gph of water circulation (between the canister and two powerheads) but this isn't a problem for my tropheus (or so I'm assuming since they are always taking turns playing in the current).
Here is a pciture of one of my tanks. My fish seem to love the current. My friend from Guatemala said that the river they are in had cuurent so I just tried to create a similar biotope. Now my pumps so shutdown at times for feeding.
Turning the water over 6 times per hour is quite reasonable. It's surprising that your fish are reacting negatively. You mentioned that this is a new filter. What kind of filter was on the tank previously? Did you just replace the filter or keep them both on the tank for several weeks? I'm wondering if you removed a lot of the beneficial bacteria when you took off the old filter and put on this one. If that's what happened, you should check your ammonia and nitrite levels. It could be that this is what your fish are reacting to.