Make sure that the partition is flagged as active, you can use the XP
Disk Management tool or a Windows 98 startup diskette and FDISK to
verify the active status of the partition. If the partition is active
but still refuses to boot it probably doesn't have a proper NT boot
sector, boot to the Recovery Console and issue the FIXBOOT command on
the disk. The cloning utility is supposed to create the NT boot sector
but it could be that the utility that you are using doesn't do this
properly. Formating the disk with the Windows XP Disk management tool
will automatically create a proper NT boot sector for the partition, it
will do this regardless of the file system that you decide to use for
the format. If the disk was formated using Windows 98 or a Windows 98
startup diskette it doesn't contain a proper NT boot sector. Unless you
need the drive to be accessible by a legacy operating system, like
Windows 98/ME, you are better off using the NTFS file system and you are
better off formating the disk NTFS immediately rather than converting it
from FAT32 later.
John