Scary problem after successful clone

[dreissk]

I had completed a successful clone of my Mac OS yesterday (10.4.11) and confirmed by booting from the drive. I then switched my startup disk back to the internal and everything worked fine. Now, however, (and this is where I need help) every time I boot my computer (the external backup isn't hooked up BTW) the computer can't find an OS and a folder with a "?" comes up against a white screen as the computer boots. If I hold down "D" everything is fine since I'm telling the computer to look for the OS on the disk but I really want it to look there automatically again. I have rebooted 5-6 times now and the problem consistently happens. The only thing I've done on the computer is the super duper clone so I believe that processed started the problem. Does anyone have any suggestions or has had this happen to them before?
Thanks for your time

[dnanian]

Are you sure you've set your startup drive to your internal using the Startup Disk Preference Pane?

[dreissk]

Yes, I believe so. I figured that after setting my startup drive back to the internal drive for boot once and then restart, it should remember my settings? Is there something else that I need to do to tell the computer to always look there first?

[dnanian]

I can't see why it would give a ? unless, perhaps, the drive is taking a long time to actually spin up.

[dreissk]

What I don't get is that if I set the startup drive back to the internal and then tell it from the pref pane to restart it'll find the OS just fine. Where it fouls up is when I try to do a normal reboot; it's only then that I get the "?"

(thanks for the help by the way)

[dnanian]

Yes - perhaps that's when the drive is taking longer to spin up...

[dreissk]

I don't know. All I know is that it's never happened before using super duper and now it's happening 100% of the time.

[dnanian]

I don't think it has anything to do with SuperDuper! - we just copy files. If you've set the startup drive with the Startup Disk Preference Pane, power your Mac off and when you start up it puts up the ? for a little while, it's just looking for the startup drive...