Are they IDE or SATA or SCSI? If you can afford it I'd go with faster SATA or SCSI disks (7200rpm, 10k rpm, 15k rpm); if the disks are turning out to be the issues it would likely be a resources issue on the machine with writing to disk (it's also prudent to let you know that even writing to MySQL writes to your hard disk, as mysql files are stored as flat files in the end).
