George -
Is the HD partitioned?
Beige models have a quirk that if the system is not within the first 8 GB of the HD, the computer will have trouble finding the system and not boot reliably, take a really long time about it, or exhibit other weirdness.
Since they shipped with 4 and 6 GB drives, most people never find out about this until they upgrade to a HD larger than 8 GB.
If this is the prob, the only fix is to copy the data off the drive (to another drive, another computer, to seedies, to zip disks, or a tape drive), boot to a seedie that contains a system (bootable OS seedie), reformat the drive into two or more partitions, re-install the system onto the first partition (which must be 8 GB or smaller), and copy the other data back onto the HD (the non-system data can go anywhere).