The reason the first disk is faster is probably alot more on the software side than hardware. It could be what's installed (more gunk => slower disk) or it could be the drive setting, like UDMA setting.
The partitioning shouldn't make a noticeable difference anyway.
I always format every few months to keep things running lean and mean. also make sure both drives are defragged and UDMA settings are correct as that like Zedric said can make differences. Huge sometimes, my motherboards defaul was PIO 4, which was painfully slow!
Ep, glad to see you come back and tidy up...did want to ask a one day favor, I want to enhance my resume , was hoping you could make me administrator for a day, if so, take me right off since I won't be here to do anything, and don't know the slightest about the board, but it would be nice putting "served administrator osnn", if can do, THANKS