OS on external firewire doesn't shut down

Hi. I have an OS for emergencies on an external firewire drive. So after updating to OSX 10.5.8 my external firewire sometimes doesn't shut down when I used it as the bootdrive, and want to switch to my internal harddrive for booting (I of course select the start up disk in system preferences before shut down or restart). On both harddrives are 10.5.8 installed. So I don't know. I have done disk verify (and repair once on the external as needed) and I have done permission repair on both pretty often. Switching from the internal to the external firewire is no problem, but switching back sometimes is. What happens is when the external shuts down, after all apps are quit (by me of course), finder, dock and all desktop icons disappear, only the mouse pointer and desktop background pic stays, and nothing else happens. I never had this problem on Tiger. I suspect a conflict between the same OSs on both drives. If I can get the firewire to shut down correctly, I am considering to always hold down the option key at start up and there select which drive to boot from, instead of doing it before in system preferences of either running OS. Any thoughts are appreciated!!

Yeah. Thanks. But I also have the same problem with my internal HD. Freezes before log out sometimes. If I reach log out, then no problem to shut down or restart. Very strange....and in fact painful turning the computer off sometimes having to press the power button 10 secs.

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    here’s the .shutdownStall report:
    Date/Time:       2014-08-28 09:36:15 +0200
    OS Version:      10.9.4 (Build 13E28)
    Architecture:    x86_64
    Report Version:  18
    Command:         No Target
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    Version:         ??? (???)
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    Pageins:         2 pages
    Pageouts:        0 pages
    Swapins:         0 pages
    Swapouts:        0 pages
    Process:         avguard-ondemand-mgmt
    Path:            /Applications/Avira.app/Contents/guard/avguard-ondemand-mgmt
    Architecture:    x86_64
    Parent:          avguard.bin
    Responsible:     avwatchdox.bin
    UID:             0
    Task size:       1042 pages (+17)
    CPU Time:        0.002s
    Importance:      Donating
    IO Policy:       Standard
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                       *1 ??? (mach_kernel + 223579)
                         *1 machine_switch_context + 354 (mach_kernel)
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             0x10eb83000 -        0x10ee85ff7  avguard.bin (0) <01F00114-EE38-3CF4-970C-6C51913B38D0> /Applications/Avira.app/Contents/guard/avguard.bin
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      101 start + 1 (libdyld.dylib)
        101 main + 3271 (avlogwriter)
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      101 thread_start + 13 (libsystem_pthread.dylib)
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      15 thread_start + 13 (libsystem_pthread.dylib)
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      101 thread_start + 13 (libsystem_pthread.dylib)
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      101 thread_start + 13 (libsystem_pthread.dylib)
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      101 thread_start + 13 (libsystem_pthread.dylib)
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             0x10fed1000 -        0x11016cfef  avqmd (0) <867ED790-C8F0-3839-BE75-E10E0884414F> /Applications/Avira.app/Contents/MacOS/avqmd
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