What application are you benching with?
For me HD Tune reports speeds on the Perc 6i that are much slower than onboard ICH Raid. I am talking less than 150 MB/S average for the Perc, and 250 for the ICH. I have screen shots.
Crystal Mark on the other hand shows almost 270+ across all tests on the Perc. Besides that, I don't need a benchmark to show me my system if faster on the Perc so I am inclined to think something is wrong with HD Tune.
This is on Circa 2008 640GB WD Caviar Black with TLER ON.
Before you go flashing firmwares, I would recommend using some other synthetic benchmarks.