If you did a backup and restore then only the active partitions were copied to your new drive. The inactive partitions do not get copied when using MFS Tools unless you do a dd copy of the specific partitions.
Now for the $64K question - Did you make your new rc.sysinit.author file executable (i.e. chmod 755 rc.sysinit.author)? If not then your HDTivo would still boot normally but your hacks would never run since the rc.sysinit.author file would not have been executed.
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