Converting File Sys to NTFS (Problems)

I recently tried to use the NT file system conversion utility convert.exe, but the process hangs right after the line where it tells you how much space is needed for the conversion. The “Converting file system” line should appear while the process runs, but it never does and the system hangs with the HDD LED blinking. I have a 12GB HDD and dual-booting with WIN98. The system partition is C and the boot partition is E. WIN98 is installed on C and Windows NT on E (this is the drive I am trying to convert). I have used the convert command before on a partition on a second HDD on this system with complete success. I have rebooted several times, but the system always hangs at the same point. Any ideas?