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Ok, once I did a restart I had no further problem dismounting the external drive.
As to the rest: I've done all you have suggested and still the external drive does not appear in the Start Up Disk window in System Preferences. I've given a few of my usual apps a go and they seem as usual. Perhaps all is well?
Regarding the bootability of the Macally drive. I was sold the enclosure by my local Mac service center on the understanding that it would be bootable. Indeed the first copy made was by them. I never tested it for bootability, so who knows...
Any further suggestions before I return to the service center and ask them to sort it out?
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