Hard drive access problems

[PSchueller]

I realize that this similar issue has been posted, but I am reposting anyway. First off, I am running Visa business 32bit. I first noticed this problem when I tried to use diskeeper. The program would defrag my servicev002 partition and my intel turbo memory, but not my main harddrive. Unlike others, I never got an error message, it would just put a progress bar in the lower right that stayed at zero, if I clicked on anything else, it would disappear. Also, I cannot perform a disk check. The message is "cannot open drive for direct access" or something similar. I have since uninstalled diskeeper in favor of PerfectDisk 2008. PD'08 can defrag my main drive, but cannot perform a boot-time defrag. I would prefer to not have to restore factory settings if possible.
Thanks in advance for any help.

EDIT: I did do a restore, uninstalled diskeeper and put on PerfectDisk, because I liked it much more. I can now do a boot-time defrag, but still no disk checking.