So I finally decided to reformat my windows 7 and redo partitions on my OS drive to allow room for a needed Ubuntu partition.
I just got 7 reinstalled, however my separate storage drive, that was unaffected throughout this is acting weird, or maybe it is the other I am not sure. Anyways the situation is, file transfers between drives are horribly slow, below 5 MB/s at most times. Google didn't seem to show up anything to fix my problem..
Both drives.. are they both SATA? If one is IDE and on the same channel as an optical drive then thats your problem right there. You may also want to check for updated motherboard drivers and BIOS updates. Its VERY unlikely its an OS problem but you can check to make sure that DMA is enabled though I'm not certain DMA settings apply to SATA drives/controllers.
Under the drive properties you can look at the policies tab. Make sure its optimized for performance and write caching is enabled.
IDE controller properties will have DMA settings in the advanced settings tab.