Problems after 10.4.4 install

I have several problems after installing 10.4.4 on my upgraded B&W G3 (Sonnet G4 1 Ghz, Sonnet ATA66 PCI Card which Boot drive is connected to)
when I run software update, any installs get to 80%-100% complete and then stops as soon as it starts to optimize. This is the same whether I use software update or install from a dmg downloaded from Apple.
I've repaired permissions, ran Diskwarrior and done 2 Archive and Installs.
I also noticed the mach_kernal file is now visible.
updating to 10.4.5 resulted in the same thing. The install stops and doesn't proceed to optimize the system. Force quitting the installer and restarting results in the system profiler reporting that I've installed the software (ie am running 10.4.5), but I've had some items become corrupted, like my Keychains.
I've installed all the latest software/firmware from Sonnet. everything was working great before the 10.4.4 update. Now I can't even do a simple software update properly.

Hector,
Assuming you have no external things connected to your machine, and this is happening, it sounds like a hardware issue in your case. In the future, please start a new topic by posting at the board level (such as the level you get to through this link) "Post a New Topic" unless you have an answer to the existing thread. That way, people won't get confused with solutions which won't apply to them, and you won't get confused which solutions which don't apply to you and neither party will get messed up trying to resolve the wrong issue. In addition, it will give your question a much wider audience that may have a good answer for your problem.

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    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.
         1. Select Disk Utility from the main menu then press the Continue
             button.
         2. Select the destination volume from the left side list.
         3. Click on the Restore tab in the DU main window.
         4. Select the destination volume from the left side list and drag it
             to the Destination entry field.
         5. Select the source volume from the left side list and drag it to
             the Source entry field.
         6. Double-check you got it right, then click on the Restore button.
    Source means the external old drive. Destination means the new internal drive.

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