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Slow start up / "ghost programs"

Update:11-30Source: network consolidation
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I had some trouble with my harddisk when it filled up and became slow, so I made a clean install and copied back my things from Time Machine. But, and this problem happened before that too, my iMac takes forever to startup (about 5 minutes).
And every now and then a program (mostly iTunes) will become non-responsive, but apparently shuts down in a normal fashion when I close it. But the symbol in the dock will say it's still running, and in a mystical way... it is. Because force shut down doesn't work, neither with any program or a restart of the finder, and the only thing working is to do a cold restart of the machine. Interestingly, the activity monitor doesn't find the programs that hangs either, even if they are running.
I don't understand a thing right now...

The Best Answer

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1. Check your Startup Disk. Go to System Preferences/Startup Disk and make sure that your Mac OS X system drive/folder is selected as your startup disk. Otherwise the system could take longer searching for it every time you boot.
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2. Repair Permissions. Open Applications/Utilities/Disk Utility select your hard drive on the left and under the First Aid tab click Repair Disk Permissions.
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3. Verify Disk. While you are in Disk Utility after you Repair the Permissions click Verify Disk. This will check the integrity of your volume directory. If there are any errors that need to be addressed you will have to boot up to your install disk in order to run Repair Disk.
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4. Check your login items list. Go to System Preferences/Accounts/Login items. If there are any Applications there that should not be simply remove it from the list.
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5. Disconnect any external devices for testing purposes. External hard drives, ipods, scanners, printers, have been known at times to cause startup/shutdown issues.
NOT DONE YET
I've bought a new 1 TB MyBook today so I can remove a Maxtor-disk I have who's been difficult to read from (it doesn't always appear in the Finder), so I'm moving my music and different stuff right now and I'll have to wait some time to do a startup without external disks. In addition I have a 500 GB LaCie with two partions (250 on each, one for Time Machine) who seems to work fine.
It's the actual start up which is the problem, not the login process.
I can live with the slow start up for now, but my main problem is when iTunes and Xtorrent freezes and starts acting like a ghost. Any ideas there? It just happened with Xtorrent again now. It's shut down, but the dock indicates that it's still running...