Hm. Well, we haven't quite isolated the smaller partition, but if the larger partition worked (I assume it's also the most recent version of the OS), perhaps you could try Smart Updating it with SuperDuper! and see ifi that boots. This isn't something I've hit before, Goldie, so sorry if there's a bit of hunting in the dark!
If not, it would help if you'd send your SuperDuper!.log (which you'll find off your Home folder in Library/Logs -- attach the file, don't copy/paste) and a System Profiler report, with the drive attached (run System Profiler, choose File | Save, then save to the default XML format), to support. I'll take a look and see if I can find any explanation.
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--Dave Nanian
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