Sounds like a corruption of some sort.
I recently did the same thing...ending up with a full backup bootable OS....only time I had any trouble was when swapping and booting with BOTH connected.....both were primary...one on the Primary IDE [the actual boot] and one on the secondary IDE [second boot]....I think it was down to the fact the system was a wee bit confused to have two 'partitions' with identical info.
The problem was in opening a file manager....everything just sat there scratching its head.....however I'm currently running with both attached....C drive and D drive are both bootable OS systems [XP Pro]....and since the 2 of them are in caddies I can switch to either or both in the time it takes to shutdown and reboot.
When I did all this I partitioned and formatted the 'D' via the original OS.....then ran Drive Image 7 ....took about 6 minutes to back up and about 8 to restore to the new one....about 6 gig of data in a 20 gig partition.
Interestingly, XP Activation appears to be happy with both....[which always had me wondering]....
The plan is to make complete 'backups' periodically so the second drive is up to date and can be used if the primary has a terminal episode.
Work data is on a third physical drive and has redundancy backups to alternate partitions on the OS drives...updated daily.
Data such as proggy skins, Litestep themes...created and modded within the OS drive's standard program Files layout are also redundantly backed up to separate physical drives.
All you need then is a weekly data off-take to CD and you're laughing.
There's no excuse for losing work....