I noticed that you ran "chkdsk" but did you run this with the /f or /r parameter? Check disk will need to be done with one of the following parameters:
chkdsk <drive:> /f
chkdsk <drive:> /r
The reason you are receiving this error is that Diskeeper is determining that your drive is in a "dirty" condition. Since data integrity is a primary concern on any hard drive, Diskeeperwill not defragment a drive in a "dirty" condition since this would risk the data on the drive.