Skipping/Poor Audio in iTunes 6.0.1

I'm getting horrible audio playback in iTunes 6.0.1 (after upgrading to both that and OS 10.4.3). Every song plays through with small hiccups/skips that are noticable and annoying. The files play fine through my iPod, so the files don't seem to be the issue. Anyone else having this problem? Any thoughts?

As a test, try playing one of the songs that are skipping using the QuickTime Player instead of iTunes. Does the problem go away once you're out of iTunes?
I'm having the same problem with iTunes 4.9. The twist is that in my case it is only happening on AIFF formatted files. mp3's and mp4's work fine, and the AIFF file plays fine in QuickTime Player.
I've tried all the recommended fixes floating around these discussion groups, but nothing fixes the problem. It is very annoying.

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    EtreCheck version: 2.1.8 (121)
    Report generated 9 Apr 2015 16:22:01 GMT+3
    Download EtreCheck from http://etresoft.com/etrecheck
    Click the [Click for support] links for help with non-Apple products.
    Click the [Click for details] links for more information about that line.
    Hardware Information: ℹ️
        MacBook Pro (Retina, 15-inch, Late 2013) (Technical Specifications)
        MacBook Pro - model: MacBookPro11,3
        1 2.3 GHz Intel Core i7 CPU: 4-core
        16 GB RAM Not upgradeable
            BANK 0/DIMM0
                8 GB DDR3 1600 MHz ok
            BANK 1/DIMM0
                8 GB DDR3 1600 MHz ok
        Bluetooth: Good - Handoff/Airdrop2 supported
        Wireless:  en0: 802.11 a/b/g/n/ac
        Battery Health: Normal - Cycle count 106
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        Intel Iris Pro
        NVIDIA GeForce GT 750M - VRAM: 2048 MB
            Color LCD spdisplays_2880x1800Retina
            2757 spdisplays_1080p
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        APPLE SSD SM0512F disk0 : (500,28 GB)
            EFI (disk0s1) <not mounted> : 210 MB
            Recovery HD (disk0s3) <not mounted>  [Recovery]: 650 MB
            Macintosh HD (disk1) /  [Startup]: 499.07 GB (6.42 GB free) (Low!)
                Encrypted AES-XTS Unlocked
                Core Storage: disk0s2 499.42 GB Online
    USB Information: ℹ️
        Apple Internal Memory Card Reader
        Apple Inc. Apple Internal Keyboard / Trackpad
        Apple Inc. BRCM20702 Hub
            Apple Inc. Bluetooth USB Host Controller
        Wacom Co.,Ltd. Intuos5 touch S
        Apple, Inc. Keyboard Hub
            Apple, Inc Apple Keyboard
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        Apogee Electronics Duet 400mbit - 400mbit max
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            Apple Inc. Thunderbolt to FireWire Adapter
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        Anywhere
    Kernel Extensions: ℹ️
            /Applications/DAEMON Tools Lite.app
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            /Applications/Parallels Desktop.app
        [not loaded]    com.parallels.kext.hidhook (9.0 24172.951362) [Click for support]
        [not loaded]    com.parallels.kext.hypervisor (9.0 24172.951362) [Click for support]
        [not loaded]    com.parallels.kext.netbridge (9.0 24172.951362) [Click for support]
        [not loaded]    com.parallels.kext.usbconnect (9.0 24172.951362) [Click for support]
        [not loaded]    com.parallels.kext.vnic (9.0 24172.951362) [Click for support]
            /Library/Extensions
        [loaded]    at.obdev.nke.LittleSnitch (4234 - SDK 10.8) [Click for support]
        [loaded]    com.Apogee.driver.DuetFWOverideDriver (1.4.4 - SDK 10.9) [Click for support]
        [not loaded]    com.wacom.kext.ftdi (1 - SDK 10.10) [Click for support]
            /Library/Extensions/HuaweiDataCardDriver_10_9.kext/Contents/PlugIns
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        [not loaded]    com.wacom.kext.wacomtablet (6.3.11 - SDK 10.9) [Click for support]
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        [running]    at.obdev.LittleSnitchUIAgent.plist [Click for support]
        [running]    com.ApogeePopup.plist [Click for support]
        [loaded]    com.google.keystone.agent.plist [Click for support]
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        [loaded]    com.roox.YotaAccess.Agent.CheckTrash.plist [Click for support]
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        [running]    HWPortCfg.plist [Click for support]
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        Open in Internet Explorer
    3rd Party Preference Panes: ℹ️
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        Flip4Mac WMV  [Click for support]
        WacomTablet  [Click for support]
    Time Machine: ℹ️
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    Top Processes by CPU: ℹ️
             6%    WindowServer
             5%    coreaudiod
             2%    studioapp
             1%    Little Snitch Agent
             1%    Google Chrome
    Top Processes by Memory: ℹ️
        292 MB    Google Chrome
        258 MB    Skype
        206 MB    studioapp
        172 MB    mds_stores
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        10.31 GB    Free RAM
        4.47 GB    Active RAM
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        0 B    Page-outs
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        Apr 9, 2015, 03:23:29 PM    /Library/Logs/DiagnosticReports/WacomTabletDriver_2015-04-09-152329_[redacted]. crash
        Apr 9, 2015, 03:23:19 PM    Self test - passed
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        Apr 7, 2015, 04:24:04 PM    /Library/Logs/DiagnosticReports/Adobe Illustrator_2015-04-07-162404_[redacted].hang
        Apr 7, 2015, 04:19:53 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/QuickLookSatellite_2015-04-07- 161953_[redacted].crash
        Apr 7, 2015, 04:19:38 PM    /Library/Logs/DiagnosticReports/WacomTabletDriver_2015-04-07-161938_[redacted]. crash
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