SUS - Some Clients Take a Long Time to Check for Updates

We have the newest XSERVE, running 10.6, with 12GB of RAM. We use it as our software update server and for some reason, some clients take a long time to check for updates. I'm talking anywhere from an 30 mins to an hour. I can't figure it out. Some clients are quick, some are extremely long.
Now if I tell the client to just check Apple for updates, it takes a few seconds.
Can anyone offer any suggestions?
Thanks.

After another restart, firefox has begun throwing errors when starting from terminal. the error reported is:
/opt/kde/bin/skim: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
This is printed 5 times, then gives up and firefox loads quickly after. So this appears to be an issue with skim and libpng similar to other problems being reported.
Some research uncovered that skim is no longer supported and is part of my kdemod3 install, however until this update it was working fine under kdemod4.

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        Hitachi HTS545032B9A302 disk0 : (320,07 GB)
            EFI (disk0s1) <not mounted> : 210 MB
            Recovery HD (disk0s3) <not mounted>  [Recovery]: 650 MB
            Macintosh HD (disk1) / : 318.84 GB (47.94 GB free) - 51 errors
                Core Storage: disk0s2 319.21 GB Online
        MATSHITADVD-R   UJ-898 
    USB Information: ℹ️
        Apple Inc. Apple Internal Keyboard / Trackpad
        Apple Inc. BRCM2070 Hub
            Apple Inc. Bluetooth USB Host Controller
        Apple Inc. FaceTime HD Camera (Built-in)
        Apple Computer, Inc. IR Receiver
    Thunderbolt Information: ℹ️
        Apple Inc. thunderbolt_bus
    Gatekeeper: ℹ️
        Mac App Store and identified developers
    Launch Agents: ℹ️
        [not loaded]    com.adobe.AAM.Updater-1.0.plist [Click for support]
        [loaded]    com.oracle.java.Java-Updater.plist [Click for support]
        [running]    com.trusteer.rapport.rapportd.plist [Click for support]
    Launch Daemons: ℹ️
        [loaded]    com.adobe.fpsaud.plist [Click for support]
        [loaded]    com.adobe.SwitchBoard.plist [Click for support]
        [loaded]    com.microsoft.office.licensing.helper.plist [Click for support]
        [loaded]    com.oracle.java.Helper-Tool.plist [Click for support]
        [loaded]    com.oracle.java.JavaUpdateHelper.plist [Click for support]
        [running]    com.trusteer.rooks.rooksd.plist [Click for support]
    User Launch Agents: ℹ️
        [loaded]    com.adobe.AAM.Updater-1.0.plist [Click for support]
        [loaded]    com.adobe.ARM.[...].plist [Click for support]
        [loaded]    com.google.keystone.agent.plist [Click for support]
        [running]    com.spotify.webhelper.plist [Click for support]
    User Login Items: ℹ️
        iTunesHelper    UNKNOWN Hidden (missing value)
        AdobeResourceSynchronizer    Application Hidden (/Applications/Adobe Reader.app/Contents/Support/AdobeResourceSynchronizer.app)
        Stickies    Application  (/Applications/Stickies.app)
    Internet Plug-ins: ℹ️
        JavaAppletPlugin: Version: Java 8 Update 31 Check version
        FlashPlayer-10.6: Version: 17.0.0.134 - SDK 10.6 [Click for support]
        Default Browser: Version: 600 - SDK 10.10
        AdobePDFViewerNPAPI: Version: 10.1.13 [Click for support]
        AdobePDFViewer: Version: 10.1.13 [Click for support]
        Flash Player: Version: 17.0.0.134 - SDK 10.6 [Click for support]
        QuickTime Plugin: Version: 7.7.3
        SharePointBrowserPlugin: Version: 14.4.8 - SDK 10.6 [Click for support]
        Google Earth Web Plug-in: Version: 7.1 [Click for support]
        Silverlight: Version: 5.1.30514.0 - SDK 10.6 [Click for support]
        iPhotoPhotocast: Version: 7.0 - SDK 10.8
    User internet Plug-ins: ℹ️
        npsf_cef: Version: sf 3.3.1.1 [Click for support]
        Google Earth Web Plug-in: Version: Unknown
    Safari Extensions: ℹ️
        DivX HiQ
        DivX Plus Web Player HTML5 <video>
    3rd Party Preference Panes: ℹ️
        Flash Player  [Click for support]
        Java  [Click for support]
        MacFUSE  [Click for support]
        Perian  [Click for support]
        Trusteer Endpoint Protection  [Click for support]
    Time Machine: ℹ️
        Skip System Files: NO
        Auto backup: YES
        Volumes being backed up:
            Macintosh HD: Disk size: 318.84 GB Disk used: 270.90 GB
        Destinations:
            Time Machine Backups [Local]
            Total size: 999.86 GB
            Total number of backups: 60
            Oldest backup: 2012-07-15 01:16:54 +0000
            Last backup: 2015-03-29 19:28:06 +0000
            Size of backup disk: Excellent
                Backup size 999.86 GB > (Disk size 318.84 GB X 3)
    Top Processes by CPU: ℹ️
            97%    rapportd
             3%    WindowServer
             1%    mds
             0%    fseventsd
             0%    distnoted
    Top Processes by Memory: ℹ️
        155 MB    Safari
        120 MB    Finder
        86 MB    rapportd
        86 MB    WindowServer
        69 MB    mds_stores
    Virtual Memory Information: ℹ️
        12.56 GB    Free RAM
        2.53 GB    Active RAM
        428 MB    Inactive RAM
        1.66 GB    Wired RAM
        1.04 GB    Page-ins
        0 B    Page-outs
    Diagnostics Information: ℹ️
        Mar 31, 2015, 06:00:15 PM    Self test - passed
        Mar 31, 2015, 01:13:05 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/Microsoft Error Reporting_2015-03-31-131305_[redacted].crash
        Mar 31, 2015, 01:05:42 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/Microsoft Error Reporting_2015-03-31-130542_[redacted].crash
        Mar 31, 2015, 12:24:33 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/Microsoft Error Reporting_2015-03-31-122433_[redacted].crash
        Mar 30, 2015, 05:45:38 PM    /Library/Logs/DiagnosticReports/Skype_2015-03-30-174538_[redacted].cpu_resource .diag [Click for details]
        Mar 30, 2015, 01:52:07 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/Last.fm Scrobbler_2015-03-30-135207_[redacted].crash
        Mar 29, 2015, 05:55:05 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/com.apple.WebKit.WebContent_20 15-03-29-175505_[redacted].crash
        Mar 29, 2015, 01:06:38 PM    /Library/Logs/DiagnosticReports/VLC_2015-03-29-130638_[redacted].hang
        Mar 29, 2015, 01:02:47 PM    /Library/Logs/DiagnosticReports/VLC_2015-03-29-130247_[redacted].hang

    Open Activity Monitor and kill this process - rapportd.
    Reinstalling OS X Without Erasing the Drive
    Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
    Reinstalling OS X Without Erasing the Drive
    Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.
    When the recovery menu appears select Disk Utility and press the Continue button. After Disk Utility loads select the Macintosh HD entry from the the left side list.  Click on the First Aid tab, then click on the Repair Disk button. If Disk Utility reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit Disk Utility and return to the main menu.
    Reinstall OS X: Select Reinstall OS X and click on the Continue button.
    Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.
    Alternatively, see:
    Reinstall OS X Without Erasing the Drive
    Choose the version you have installed now:
    OS X Yosemite- Reinstall OS X
    OS X Mavericks- Reinstall OS X
    OS X Mountain Lion- Reinstall OS X
    OS X Lion- Reinstall Mac OS X
         Note: You will need an active Internet connection. I suggest using Ethernet
                     if possible because it is three times faster than wireless.

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