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Originally Posted by nekokami
"Every second time" sounds suspiciously like hardware. You might want to run fsck on the disk.
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Is it useful to run fsck if I run "Verify Disk" from "Disk Utility" and it comes up clear? (I just realised, I haven't actually done that, but I'm about to). Do I need to reboot into "safe mode" or from the OS X install disk to do this "properly"?
I hope it's not hardware. I think this is just out of warranty (it's about 12 months old).
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Originally Posted by nekokami
It is unlikely that you'll need to reinstall the OS, nor would that probably help unless you reformat the hard drive first.
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I'd had a google, and for this problem there was a bit of "install OS X again in a new spot on the disk, and alter your option to boot from there accordingly" (I believe this process will copy many of your settings across too). I haven't looked at it properly yet though, to see if it's relevant. I hate reinstalling OSs.
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Originally Posted by ShortNCuddlyAm
Had you installed the scanner shortly before the problem started?
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No. The scanner has been installed, and I've been using (with the Epson software) for some time.
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If not, have you done anything else to the system just before it started?
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It was the Vuescan software that was recently installed, some scanning software better than the manufacturer's.
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Does it happen if the scanner is turned on? (Can you turn the scanner on independently of the Mac being on? Only asking as mine takes its power from the Mac)
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Mine (Epson Perfection 4990) doesn't take power from the Mac, so, yes, it turns on independently. I'll give that a go, as there's no real reason to turn the scanner off anyway (it's just a power-aware habit, and I'm willing to lose a few carbon credits to establish if that's the cause
).
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Check if there is updated software for the scanner.
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I'll do that. I'm pretty sure that I checked when I first installed it on the iMac, but that was about 8 months ago.
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Might be worth checking if there are any updates for OS X, too.
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Definitely up-to-date there.
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Oh, and back up your data 
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Always. Photos mostly, backed up on two external hard disks, the laptop, and my old iPod Photo. The scans aren't backed up quite as much (just on the external hard disks), but then I have backups there in the form of negatives stored in archival folders.
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(And yes, I know you're an ex-IT person so you've probably thought of all of that anyway!)
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Am and Neko, it is very much appreciated. Putting aside that coming up on two years retirement has quickly refiled any skills I had (predominantly in an MS world) down in the back stacks, there's also my complete lack of familiarity with troubleshooting OS X, and that even while you might be restating what to you is "the obvious", to me it's an "obvious" step that I can quite easily and quickly miss while hunting down the wrong path.
Cheers,
Marc