I would recommend you run 10 benchmarks for each type (native SATA vs. eSATA bracket) and then average out the results. If the numbers are consistently different/lower, then I don't have an explanation. Else it's completely possible Windows was doing some form of I/O to/from the drive in the middle of the benchmark -- this happens all the time.
You are right. I just have retested again and the results are different. So as i understand it is better to get PCI eSATA controller card. I have checked out Newegg, and i can get one for $13 shipped ( Free shipping with shop runner membership) »www.newegg.com/Product/P ··· 823&SID=