Could permissions cause startup problems?

Question

Based on some strings I found about problems with permissions that some have had when upgrading to leopard, I'm suspecting permissions are the cause of my computer's not recongnizing my primary drive on startup.
I had been fiddling with permissions of several users on the computer, trying to set up an itunes library in the shared folder that all could access. I'm running tiger but some folks in this discussion area seem to be the ones knowledgeable about permissions.
Now I can only boot up from my secondary drive (which has panther installed) or from my tiger dvd. The main drive shows up as a startup choice in both places, but it doesn't work. I repaired permissions with DU but no help. The main drive does NOT show up as a choice when I do a restart / hold option key.
Is it possible that some change I made to permissions settings has caused this? If so, can someone tell me what I would do to set them right? The main drive shows up on my secondary's desktop, and the contents are completely accessible that way.
Also, I already did a re-install of tiger, but retaining the settings -- not a clean install. That changed nothing. (really really don't want to start from scratch with a clean install, but if I must...) The main drive itself, in terms of hardware, seems to be fine according to both the DU and diskwarrior.

Answer 1

I'm pretty sure i have a duplicate an not a clone, on my external drive, and yes thank goodness I've got those copies of all my files in case things go way bad.
Ok, to recap and update: Computer has a primary drive running tiger, a secondary drive running panther and a tiger installation disk in the tray. I lost the ability to boot up the primary, and I think there is a strong chance it has something to do with permissions settings gone awry. I was messing with user permissions while trying to set up a common itunes library for multiple users before the problem started. (I respect you feel that's unlikely Kappy, you're probably right, but if it's possible... I want to know if there's an option that avoids losing my settings.)
Under a normal restart, the computer chooses the install disk. Both drives show up in the install disk's startup utility. I can choose the secondary and startup to it. (and the primary shows up on the desktop.) When I choose the primary as the startup, no go -- it starts up to the install disk.
I used DU to repair persmissions on the primary drive, and also ran DU's repair disk, and Diskwarrior. The tests indicated the drive is just fine, but none of that helped a bit. I reset the p-ram and the nvram -- no help. The primary also shows up when I open the startup system pref on the secondary, but choosing it does not work -- restarting still boots to the install disk. The primary does NOT show up as an option when I do a restart / option key.
I did an archive and install from the tiger disk, retaining my settings (so the system updates are now gone) -- no help, still won't boot. I really really want to avoid an archive and install choosing to delete settings. There are several users on there, and it would take a lot of time and trouble to put humpty together again.
Here is something I found in discussions, could this help me? --
Get the Mac to set up an additional administrative account. You can then change your old account. I've tried this in 10.4.10 without problems.
This was Posted by: JoseAranda at September 9, 2006 3:48 AM
OK, restart your computer, hold down Command-s and type in the following:
/sbin/fsck -y Enter
/sbin/mount -uaw Enter
rm /var/db/.applesetupdone Enter
# The rm command is the remove command which deletes the file.
# Robert: I'd rename the file via: mv /var/db/.applesetupdone /var/db/.applesetupdone.old
reboot Enter
Once you've done that the computer reboots and it's like the first time you used the machine. Your old accounts are all safe. From there you just change all other account passwords in the account preferences!!
end of posted by: JoseAranda
http://www.askdavetaylor.com/howdo_i_reset_my_mac_os_x_admin_rootpassword.html
You will need to scroll down to see this post. Search for applesetupdone
--Could creating an additional admin account, (which would have properly configured permissions,) make the drive bootable again? I'm not an advanced computer person, not much experience working in the terminal or open firmware, but I can follow directions. If I followed the above advice to create an additional admin account, how would I know if I was creating it on the primary or the secondary drive? I notice there is a terminal utility on the tiger disk, coud I type in the commands there?
Or if the above is unlikely to help, is there something else I could do through the terminal that could repair or reset any user/ admin / persmission settings on the drive that might be causing its unbootability?