Apps like Mail and Safari Freeze initially

So I have Mac Os X Lion. I love it all around. There is just one annoying problem. When I turn my computer on, and Mail starts up, I cannot "click" on anything. The cursor moves, I can move to and click on things in other applications, but Mail and Safari often will not allow me to click. Let me be clearer. Mail is open, new messages download, the App seems to be running fine. But if I want to open a new message, no amount of clicking will open the message. Similarly, when I go to Safari, a page may load but then I cannot click on any links on the page. If I just press Command Q and reopen the program, everything is fine. But it is slightly annoying to have to do this. Any suggestions?

Hi David
I have exactly the same issue with Mail but not Safari on my MacBook Air with Lion.  I can't even use Command Q, I have to Force Quit to get Mail responding again.
I have a support call booked for Thursday night so I'll hit you up again with what they tell me.
Regards
Russ in Sydney

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              Mac Pro - model: MacPro4,1
              1 2.66 GHz Quad-Core Intel Xeon CPU: 4 cores
              8 GB RAM
    Video Information:
              NVIDIA GeForce GT 120 - VRAM: 512 MB
    Audio Plug-ins:
              BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
              AirPlay: Version: 1.9 - SDK 10.9
              AppleAVBAudio: Version: 2.0.0 - SDK 10.9
              iSightAudio: Version: 7.7.3 - SDK 10.9
    Startup Items:
              DynDNSUpdater: Path: /Library/StartupItems/DynDNSUpdater   these may be a problem. See comments below.
              EyeConnect: Path: /Library/StartupItems/EyeConnect
              ProTec6b: Path: /Library/StartupItems/ProTec6b
              VirtualBox: Path: /Library/StartupItems/VirtualBox
    System Software:
              OS X 10.9 (13A603) - Uptime: 0 days 1:6:49
    Disk Information:
              HL-DT-ST DVD-RW GH41N
              WDC WD6400AAKS-41H2B0 disk1 : (640.14 GB)
                        EFI (disk1s1) <not mounted>: 209.7 MB
                        MacPro HD (disk1s2) /: 639.28 GB (305.06 GB free)
                        Recovery HD (disk1s3) <not mounted>: 650 MB
              Hitachi HDS721010CLA332 disk0 : (1 TB)
                        EFI (disk0s1) <not mounted>: 209.7 MB
                        Internal 1TB HD (disk0s2) /Volumes/Internal 1TB HD: 999.86 GB (16.64 GB free)
    USB Information:
              Apple Computer, Inc. Apple Cinema Display
              Apple, Inc. Keyboard Hub
                        Logitech USB Receiver
                        Apple, Inc Apple Keyboard
              Apple Inc. BRCM2046 Hub
                        Apple Inc. Bluetooth USB Host Controller
    FireWire Information:
              Initio ST380013A 400mbit - 400mbit max
                        disk3s1 (disk3s1) <not mounted>: 32 KB
                        80GB MadDog (disk3s3) /Volumes/80GB MadDog: 79.89 GB (1.89 GB free)
              Oxford Semiconductor Ltd. OXFORD IDE Device 400mbit - 400mbit max
                        disk5s1 (disk5s1) <not mounted>: 32 KB
                        disk5s2 (disk5s2) <not mounted>: 51 KB
                        OWC Mercury Express (disk5s3) /Volumes/OWC Mercury Express: 20 GB (1.5 MB free)
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                        disk2s2 (disk2s2) <not mounted>: 29 KB
                        disk2s3 (disk2s3) <not mounted>: 29 KB
                        disk2s4 (disk2s4) <not mounted>: 29 KB
                        disk2s5 (disk2s5) <not mounted>: 29 KB
                        disk2s6 (disk2s6) <not mounted>: 262 KB
                        disk2s7 (disk2s7) <not mounted>: 262 KB
                        disk2s8 (disk2s8) <not mounted>: 262 KB
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              com.Logitech.Control Center.HID Driver          (3.2.0)
              com.Logitech.Unifying.HID Driver          (1.1.0)
              org.virtualbox.kext.VBoxDrv          (4.2.6)
              org.virtualbox.kext.VBoxUSB          (4.2.6)
              com.rogueamoeba.InstantOnCore          (6.0.4 - SDK 10.8)
              com.logmein.driver.LogMeInSoundDriver          (1.0.2 - SDK 10.5)
              com.Cycling74.driver.Soundflower          (1.5.3 - SDK 10.6)
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              [loaded] com.acquia.drupal.mysql0.plist
              [loaded] com.adobe.fpsaud.plist
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              [loaded] com.quark.quarkupdate.plist
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              [loaded] com.adobe.AdobeCreativeCloud.plist
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              EyeConnect
              Flash Player
              Flip4Mac WMV
              Logitech Control Center
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              Microsoft Mouse
              MusicManager
              Quark Update Preferences
              WacomTablet
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              AdobePDFViewerNPAPI: Version: 11.0.04 - SDK 10.6
              Flash Player: Version: 11.9.900.152 - SDK 10.6
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              WidevineMediaOptimizer: Version: 6.0.0.12607 - SDK 10.7
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              iPhotoPhotocast: Version: 7.0
              QuickTime Plugin: Version: 7.7.3
              FlashPlayer-10.6: Version: 11.9.900.152 - SDK 10.6
              AdobeAAMDetect: Version: AdobeAAMDetect 2.0.0.0 - SDK 10.7
              AmazonMP3DownloaderPlugin: Version: AmazonMP3DownloaderPlugin 1.0.17
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              LogMeIn: Version: 1.0.961 - SDK 10.7
              Default Browser: Version: 537 - SDK 10.9
              Flip4Mac WMV Plugin: Version: 2.4.2.4
              SharePointBrowserPlugin: Version: 14.1.4 - SDK 10.6
              WacomSafari: Version: 1.1.0-5
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              fbplugin_1_0_3: Version: (null)
              DazzboardNPAPIPlugin: Version: 0.9.18
              fbplugin_1_0_1: Version: (null)
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              DockPlistEdit:          Version: 7.0 - SDK 10.5
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              Microsoft Chart Converter:          Version: 14.1.4 - SDK 10.5
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              Microsoft Clip Gallery:          Version: 14.1.4 - SDK 10.5
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              Microsoft Database Utility:          Version: 14.1.4 - SDK 10.5
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              Microsoft Document Connection:          Version: 14.1.4 - SDK 10.5
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              Microsoft Excel:          Version: 14.1.4 - SDK 10.5
                        /Applications/Microsoft Office 2011/Microsoft Excel.app
              Microsoft Graph:          Version: 14.1.4 - SDK 10.5
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              Microsoft Language Register:          Version: 14.1.4 - SDK 10.5
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              Microsoft Office Reminders:          Version: 14.1.4 - SDK 10.5
                        /Applications/Microsoft Office 2011/Office/Microsoft Office Reminders.app
              Microsoft Outlook:          Version: 14.1.4 - SDK 10.5
                        /Applications/Microsoft Office 2011/Microsoft Outlook.app
              Microsoft PowerPoint:          Version: 14.1.4 - SDK 10.5
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              Microsoft Upload Center:          Version: 14.1.4 - SDK 10.5
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              Microsoft Word:          Version: 14.1.4 - SDK 10.5
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              My Day:          Version: 14.1.4 - SDK 10.5
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                   1%          WindowServer
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                   0%          LCCDaemon
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    12/17/13 12:31:17.132 PM Adobe Illustrator[231]: CoreText performance note: Client called CTFontCreateWithName() using name "Arial" and got font with PostScript name "ArialMT". For best performance, only use PostScript names when calling this API.
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    12/17/13 12:40:05.600 PM WindowServer[114]: device_generate_lock_screen_screenshot: authw 0x0(0), shield 0x7fb189ddd3b0(2001)
    12/17/13 12:40:05.601 PM WindowServer[114]: device_generate_desktop_screenshot: authw 0x0(0), shield 0x7fb189ddd3b0(2001)
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    12/17/13 12:43:46.758 PM WindowServer[114]: CGXSetWindowListSystemAlpha: Invalid window 157 (index 0/1)
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    12/17/13 12:44:02.081 PM com.apple.launchd.peruser.502[172]: (com.apple.mdworker.shared.01000000-0000-0000-0000-000000000000[471]) Exited with code: 75
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    12/17/13 12:44:40.829 PM WindowServer[114]: disable_update_timeout: UI updates were forcibly disabled by application "Console" for over 1.00 seconds. Server has re-enabled them.
    12/17/13 12:44:41.949 PM WindowServer[114]: common_reenable_update: UI updates were finally reenabled by application "Console" after 2.12 seconds (server forcibly re-enabled them after 1.00 seconds)
    12/17/13 12:44:47.000 PM kernel[0]: ALF: ifnet_get_address_list_family error 12
    12/17/13 12:47:44.287 PM mdworker32[510]: CGSConnectionByID: 0 is not a valid connection ID.
    12/17/13 12:47:44.287 PM mdworker32[510]: CGSGetSpaceManagementMode: No connection with id 0x       0

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