Boot up uses the registry from a different drive on a dual boot system

Last week I was having a slowdown problem on the drive I use as my primary. I did all kinds of testing to try to determine the cause but came up empty handed. All the while, I was running SFC repeatedly because it kept finding corrupt files. I shut down last night and when I rebooted this morning, the desktop itself is the one from the other secondary hard drive while the task bar is the correct one. However, programs I normally run that are in the taskbar and desktop that aren't on the secondary drive, won't run any more. After checking, I find that Vista is using the registry from the secondary drive while the contents of all my partitions (3) on the primary are correct.