I'm running SME server 6 and I'm having exactly the same problem. I only use one IDE drive, and I've never had this problem in the past 3 years.
I've connected a subdomain to an I-bay, and afther that the server rebooted. We'll, not quite actually. It stops at the 'enabling swap space' message....
Please let me know how I can fix this! I'm planning to upgrade to SME server 7 pre4 but I have to make backups first...