Getting Weird OS Behavior

I've been setting up my new Mac Pro. I removed the HD that came with the computer since I bought a larger drive (WD6400AAKS, low level formatted writing zeros once). Instead, I cloned over a drive (with SuperDuper) that was in a 1st gen Mac Pro running 10.4.11 onto that WD HD (cuz it had lots of things installed on it that I wanted to just bring over), then upgraded the OS to 10.5.4 from the Leo discs that came with my Mac Pro. Before the Leo upgrade, I ran DiskWarrior on it to clean up any issues before cloning.
Suddenly, I'm having the following issues:
--Can't use Restart... or Shutdown... unless I hold the option key so the Mac will go straight to it.
--Force Quit menu does not appear at all, though I can still force quit in Activity Monitor.
I've run Applejack on it, switched keyboard and mouse to the one that came with the Mac Pro (I'm using an older Apple keyboard that I like better), and removed all user-installed preference panes.
By coincidence or not, I don't think I started having these problems until I ran MacPar Deluxe. Basically, MPD was acting strangely, then I noticed I couldn't quit it (quit was greyed out) which is when I noticed I couldn't use Force Quit. The only issue I did notice from the get go was that the boot drive's window wouldn't stay in List view even though I've set it to do so multiple times. (Incidentally, I've since learned that MPD has some bad issues in its current 64-bit mode, so the developer issued a patch to knock it to 32-bit. I applied it, but MPD still doesn't work.)
On this last time I had funkiness, I launched Safari to type this thread, hit Login, then Safari crashed and the OS took me to the login screen. I've spent a lot of time configuring this box and am on the cusp of being able to use it for what I do and now find myself pretty frustrated. Obviously, I'm trying to avoid starting over with the boot drive.
Any clues?
Edit: I put in the original boot drive that came with the machine and noticed that the startup is significantly quicker. On this boot, the desktop came up and was ready within maybe 5 seconds at the most. On the cloned boot, the desktop would be fully functional in about 10 seconds or so. Also don't have issues with the menu nor Force Quit.
Message was edited by: MyKidsDad
Message was edited by: MyKidsDad

Hi! Sounds like the problem could be if the original Mac Pro's OS was installed using machine specific disks and then upgraded the newer one may not have all its needed os files IF it came with an installed later OS version which it would have if it is a later model. That's just a guess. I think I would use the Leopard disk and do an Archive and Install which should leave most if not all of your stuff intact. Tom

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