Hi,
Signed in specifically to reply to your problem, Psykamaholik.
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I've been doing computing since 1971, and my first decent personal computing ownership experience started with Microware OS9 (a UNIX clone) on a Radio Shack Color Computer 3. I am presently the only Macintosh Technician in my town, and I've seen your kind of problem before. Sometimes it is bad media on the Boot-drive, sometimes it is bad software in the OSX, and sometimes it is hardware related. If your problem is hardware related, you are toast. No fix but hardware replacement.
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Now let's see if we can fix this without getting really depressing <grin>!
1). Firstly, it is NEVER a good idea to "clear free space" on a drive with an existing system (anybody that says otherwise, is opening your system for obscure system or media errors that cannot be easily solved, better to stay away from it altogether, except to setup a new drive). One only does this on a clean drive, newly formatted, and only on a drive you have recently bought new. This task is the only way to make sure that the newly manufactured drive is cleanly formatted and that all the media actually works (hard errors are trapped out by "Clear Free Space"). "Clear Free Space" not only writes clean tracks/sectors, but also tests and maps out bad clusters (that's why the drive becomes unusable if the routine FAILS before completion. The mapout table file is now the authority, and it's full of junk).
If you MUST "Clear Free Space" on an existing boot-drive with an existing system; first perform a working Backup with Carbon Copy Cloner or equiv, then Format the boot-drive, then Clear Free Space, then Carbon Copy Cloner from Backup to boot-drive.
Even when "Clear Free Space" actually works with a drive that contains a system, drive performance suffers drastically, and one cannot easily get your original performance restored.
2). "Clear Free Space" on a secondary drive, done from a boot-drive tends to transfer any problems on the boot-drive to the secondary drive under test (this problem is quite rare, but it does happen). This is why you are running into big trouble with your secondary drives. Something is hinky on your boot drive (boot-drive is working because the system was installed without incident, but is not working on the secondary drive because problems that have invaded the boot-drive [after system install] are now transferred to the secondary drive where the system does NOT exist.)
I realize this sounds like gobbledygook, but while this kind of problem is not common, it MUST be dealt with by prevention. It cannot be easily repaired after the fact.
SO WHAT DOES ONE DO WITH PROBLEMS LIKE THIS?
1). First, make absolutely sure your boot drive has no problems on it. Disk Utility (even run from the OSX install DVD) cannot fix your kind of trouble. This must be looked at by a good quality 3rd party expert repair tool like "TechTool Pro", or "Drive Genius". Even then, rare problems might not be caught.
If you really need to be quite sure, first perform a bootable backup with "Carbon Copy Cloner" (or equiv). Confirm you can boot from your backup. Then (while booted from your backup), format your boot-drive and THEN perform a "Clear Free Space" which will write controlled data to all sectors which might otherwise produce binary boundary errors that can transmit to another drive invisibly thru the OSX.
If there are any doubts at all about your Installed OSX on the Backup (bad drivers, corrupt disk management that still basically works on your boot-drive), skip the previous boot from your Backup (except to insure you can boot from it), and run your OSX Installer DVD, and use the Disk Utility on the DVD (known good, right?) to perform the "Format" and "Clear Free Space" on your boot-drive.
As an aside, it is a VERY good idea to Format using the Partition Screen window (only available when the drive device hardware is highlighted instead of the partition under the device in the main left table) in Disk Utility (selecting only one(1) partition, don't leave it in the pre-existing condition in the pull-down, because any errors in the partition table will only be erased by re-establishing the table by selecting the number of partitions [normally 1]), rather than doing this via the Erase screen (big no-no, only use Erase when you are sure both the boot-drive and the new drive is otherwise "good").
Now boot from your Backup and do "Carbon Copy Cloner" back to your boot-drive. This should put your system back to rights (barring errors in the backed up OSX system).
Worst case scenario requires Cold Install of your Bootable OSX Installer DVD to a Backup Drive, and using that with the automatically called up Migration Assistant, to transfer your files and Security Data (from your boot-drive, assuming you haven't erased it yet). Then do all the updates. Now, do all the tasks to clean up your boot drive, and do Carbon Copy Cloner to the Boot-Drive. Now everything clean. If boot-drive erased, second backup drive will need to be used to install system, Migration Assistant now points to existing first Backup. Migration Assistant only works on Firewire with 10.4.x, but can work with USB too on 10.5.x or later.
To establish a secondary drive (or external Backup drive), and be absolutely certain the thing will Format and Clear Free Space, do the setup of your new drive by starting up from your Bootable OSX DVD, and use Disk Utility from there. If THAT does not work for any reason, computer hardware failure or aging is a REAL possibility.
If, after any or all of the previous, you still can't get the secondary drive to format and Clear Free Space, NOW you ARE dealing with a computer hardware problem or failure. And that means trying to initialize and start over with your boot-drive, from scratch may prove difficult or problematic in the future too.
I have run into several computers that are getting tired or worn, and will overheat and freeze-up in the middle of critical operations like "Clear Free Space"; which can bash your boot-drive, or any other drive, for that matter. MacOSX normally never freezes. Only tired hardware (works sometimes, but overheats and freezes without warning) can cause this.
I hope I've been helpful, and not too depressing. Good luck, leave no possibility unturned. You may get lucky and figure this thing out.
-Paul Pollock