First you want to create a system restore, then if you have it, use Shane's registry back up program to back up your registry.
Note: The registry is the backbone for windows to operate correctly. If the wrong key is changed or deleted, it could render your system useless. So take your time and check and then double check you are on the right key's in the registry.
Secondly make sure the option for chkdsk is unscheduled in diskeeper. Then if your on windows 7 (it should be the same for vista) go to.....
1. Click on start button.
2. In search field type "run" and click on it.
3. In run typ "regedit" click ok .
4. Go to "HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager" which means
Click HKEY_LOCAL_MACHINE
Click SYSTEM
Click CurrentControlSet
Click Control
Click Session Manager
5. In the right hand pane double click on " BootExecute".
6. The default value for the key should be "autocheck autochk *" if not, make it so.
I have attached a copy of what it should look like.
I use to use diskeeper myself and had the same problem before. I have also stopped using diskeeper because it stopped working correctly for calling the trim command on ssd drives (at least on mine it did). If you are on windows 7, it will call the trim command without a third party defragmenter any way, if you have the correct drivers loaded in the bios (google ide versus ahci for ssd drives, it will tell you all about it), I only used it to defragment my hdd's (I have 4). I have learned its just unnecessary as windows own disk defragmenter in windows 7 works pretty well.
Good luck and take care
Chris