scsi hdd boot failure

we have SCSI HDD which boots with windows 98SE it was server windows 2000 previously since it was not bootint we formatted & tried to re installed Server windows 2000 but it is not booting/Loading,But it boots with windows 98.
for server installation it copies few files & error message is displayed to run CHKDS/F,we did it but still problem is not solved.Please let us out of this situation.