Persistent Flashing Question Mark Folder Icon, after Repair & Rebuild-THX!

Hello All,
Thank you in advance for any insights.
For the past week, one/two days after a force re-boot, my Quicksilver Mac (OSX 10.4.11 and OS 9 Classic) starts up with the dreaded flashing question mark folder.
The start up disk has always been on "Mac OS X, 10.4.11 on main stuff" ("main stuff" is the name of the hard drive.)
The first time, I ran DiskWarrior and rebuilt the hard drive, which is kind of new as it was replaced in April 2009. Then I ran OnyX and got a clean bill of health. The Mac was shut down at the end of the day as is my habit via turning off the power strip.
If it helps, here's part of the DiskWarrior report:
• 13 files had a directory entry with an incorrect text encoding value that was repaired.
• 340 files had a damaged extended attribute that was repaired.
• 3 folders had a directory entry with an incorrect custom icon flag that was repaired.
• Incorrect values in the Volume Information were repaired.
Disk Information:
Files: 370,719
Folders: 85,161
Free Space: 92.55 GB
Format: Mac OS Extended (Journaled)
Block Size: 4 K
Disk Sectors: 268,171,472
Media: WDC WD5000AAKB-00H8A0
The next day, the flashing question mark folder reappeared. This time I used the original system installer CD (labeled Power Mac G4 OS X Install). Disk Utility made its repairs. And this time, the computer was put to sleep instead.
In the morning, it woke up, the wireless optical mouse worked for a few seconds, the hard drive is humming along then all of a sudden the arrow (mouse) froze and none of the keys on the keyboard functioned.
After some research, I deleted the energy saver preference (powermanager.list?) and ran Disk Utility again. And again, I shut down b/c I wasn't going to use the Mac for a day or two.
This afternoon, the pesky icon reappeared at start up. At first Disk Utility didn't see the hard drive then I restarted and the hard drive was selectable though not mounted. It was repaired and verified yet once again. Btw, when I did hard drive test, the message says something to the effect that it appears to be working properly.
My question is, might anyone know what's wrong? I've been backing up after every use and I have a laptop. But I love working on the desktop and if this issue can be fixed, that would be perfect.
As an aside, I've read that I should do a clean install. Would doing a clean install mean I need to re-install OS 9 as well as all other all other software programs-Adobe Creative Suite, Quickbooks, Verizon DSL, printer drivers etc.?
One final question, can I continue to boot up from the CD, repair then restart or will I damage the computer? Once it restart, everything seems to work normally and well.
Many, many thanks for reading and any help would be greatly appreciated!
Have a wonderful weekend.
Sam

Disk damage can also affect the startup sequence, but I think what you have already done should have repaired any disk damage, or given you more information.
Once you have ruled out Disk damage, you get the flashing question mark when your Mac cannot find:
• the preferred operating System
• of the preferred version
• on the preferred startup drive.
All these items are stored in the parameter RAM, backed up by a 3.6 volt, non-recharging 1/2-AA size battery that lasts three years or so, unless you turn off all power at night.
If you cannot remember when you last changed that battery, now is a good time. Be sure to reset the PMU/PRAM after installing the new battery.
Message was edited by: Grant Bennet-Alder

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    Note that the information I have provided is what Apple recommends, If other users suggest different solutions than found here, then be sure what they recommend does not impact on your warranty, if any, or ability to get continuing Apple service.
    Please don't start removing drives or changing cables unless you know what you are doing and have exhausted other non-invasive alternatives outlined here. If you perform any work yourself that is unapproved by Apple, then you will void any warranty you may have and lose all further Apple Support.
    Repair the Hard Drive and Permissions
    Boot from your Snow Leopard Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer.
    If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
    The main difference if you are using Lion or Mountain Lion is that you must first boot from the Recovery HD. Simply boot from the Recovery HD to perform the above.
    Reinstall Snow Leopard Without Erasing The drive
    1. Repair the Hard Drive and Permissions
    Boot from your Snow Leopard Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer.
    If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
    2. Reinstall Snow Leopard
    If the drive is OK then quit DU and return to the installer.  Proceed with reinstalling OS X.  Note that the Snow Leopard installer will not erase your drive or disturb your files.  After installing a fresh copy of OS X the installer will move your Home folder, third-party applications, support items, and network preferences into the newly installed system.
    Download and install Mac OS X 10.6.8 Update Combo v1.1.
    Reinstalling Lion/Mountain Lion Without Erasing The Drive
    Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
    Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.
    When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the main menu.
    Reinstall Lion/Mountain Lion: Select Reinstall Lion/Mountain Lion and click on the Continue button.
    Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.

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