Time Machine Preferences breaks when I wake from sleep

I have recently started having a problem.
When I start my computer, everything is functioning fine. I am able launch System Preferences and open any preference pane and quit System Preferences and everything is fine.
When I put my computer to sleep and then wake it up, I have issues. If I open System Preferences, I can close it. If I click on Trackpad, I can close it. But if I click on Time Machine Preferences and try to quit System Preferences, it doesn't quit. If I try to Force Quit, I get the standard "this app isn't responding" error box.
I cannot quit System Preferences is any way. Force Quit does nothing and eventually the rest of my apps on my machine stop functioning. I have to hard reset my machine to get System Preferences back.
Anyone else seen this? I don't want to blame it on 10.5.6 but I think that this started happening after that.

So I have made a further discovery.
It is related to my non-Time Machine external hard drive. When it is connected I have the issue mentioned above, when it's not connected I have no problem. I re-formatted the drive and no longer have the issues with the System Preferences, but now, if I sleep, when I wake I can't shut down. It just hangs and I have to hard restart.
A couple of notes from the console log. When the "bad" drive is hooked up, I see the following message (multiple times when I wake up:
*kernel AppleYukon2: 00000000,00000000 sk98osx_dnet - recovering from missed interrupt*
Also, when I try to do the actual shutdown, I see this error:
*/usr/sbin/kdcmond[37] dnssd_clientstub read_all(3) failed 0/28 0*
So I feel like the issue is somehow connected to my eternal drive having a conflict with the wired network card. I am going to do some more tests.

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