Apple Mail smart mailboxes no longer work

Well, the subject says it all.
I am running Mail 7.3 under Mac OS X 10.9.5 and have 8 smart mailboxes set up. However, as of this morning, none of them are displaying any emails, along with all the VIPs. However, all other folders etc are working normally.
Any suggestions anyone?
Joe.

Ok, so I was right about the Combo updater - wouldn't install on my system.
So I tried all your other suggestions (well, except for installing Yosemite) and no go, although I'm not sure that resetting my file and folder permissions worked properly (I waited 15 mins and still didn't get the 'reset' button back again, so I just continued on with the rest of the steps).
Here is my Etrecheck results:
EtreCheck version: 2.1.8 (121)
Report generated 23 March 2015 9:59:21 pm AEST
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
    iMac (21.5-inch, Mid 2010) (Technical Specifications)
    iMac - model: iMac11,2
    1 3.06 GHz Intel Core i3 CPU: 2-core
    12 GB RAM Upgradeable
        BANK 0/DIMM0
            2 GB DDR3 1333 MHz ok
        BANK 1/DIMM0
            4 GB DDR3 1333 MHz ok
        BANK 0/DIMM1
            4 GB DDR3 1333 MHz ok
        BANK 1/DIMM1
            2 GB DDR3 1333 MHz ok
    Bluetooth: Old - Handoff/Airdrop2 not supported
    Wireless:  en1: 802.11 a/b/g/n
Video Information: ℹ️
    ATI Radeon HD 4670 - VRAM: 256 MB
        iMac 1920 x 1080
System Software: ℹ️
    OS X 10.9.5 (13F1066) - Time since boot: 0:12:30
Disk Information: ℹ️
    ST3500418AS disk0 : (500.11 GB)
        EFI (disk0s1) <not mounted> : 210 MB
        Macintosh HD (disk0s2) / : 499.25 GB (190.97 GB free)
        Recovery HD (disk0s3) <not mounted>  [Recovery]: 650 MB
    OPTIARC DVD RW AD-5680H 
USB Information: ℹ️
    ASMedia AS2105 1 TB
        EFI (disk2s1) <not mounted> : 210 MB
        Digital Media (disk2s2) /Volumes/Digital Media : 999.86 GB (274.31 GB free)
    Samsung M3 Portable Samsung M3 Portable 2 TB
        EFI (disk1s1) <not mounted> : 210 MB
        iMac 2TB TM Backup (disk1s2) /Volumes/iMac 2TB TM Backup : 2.00 TB (753.92 GB free)
    Apple Inc. BRCM2046 Hub
        Apple Inc. Bluetooth USB Host Controller
    Apple Internal Memory Card Reader
    INNO TECH USB to Serial
    Apple Inc. Built-in iSight
    Apple Computer, Inc. IR Receiver
Gatekeeper: ℹ️
    Anywhere
Kernel Extensions: ℹ️
        /Library/Application Support/VirtualBox
    [loaded]    org.virtualbox.kext.VBoxDrv (4.3.20) [Click for support]
    [loaded]    org.virtualbox.kext.VBoxNetAdp (4.3.20) [Click for support]
    [loaded]    org.virtualbox.kext.VBoxNetFlt (4.3.20) [Click for support]
    [loaded]    org.virtualbox.kext.VBoxUSB (4.3.20) [Click for support]
        /Library/Extensions
    [loaded]    com.usboverdrive.driver.hid (3.1 - SDK 10.8) [Click for support]
        /Library/Extensions/USBOverdrive.kext/Contents/PlugIns
    [loaded]    com.usboverdrive.driver.bt (3.1 - SDK 10.8) [Click for support]
    [not loaded]    com.usboverdrive.driver.hid.safe (3.1) [Click for support]
        /System/Library/Extensions
    [not loaded]    com.Belcarra.iokit.USBLAN_netpart (3.1.1 - SDK 10.6) [Click for support]
    [not loaded]    com.Belcarra.iokit.USBLAN_usbpart (3.1.1 - SDK 10.6) [Click for support]
    [not loaded]    com.RemoteControl.USBLAN.usbpart (3.1.1 - SDK 10.7) [Click for support]
    [loaded]    com.orderedbytes.driver.ControllerMateFamily (4.6.0 - SDK 10.6) [Click for support]
    [loaded]    com.squirrels.airparrot.framebuffer (3 - SDK 10.7) [Click for support]
    [loaded]    com.squirrels.driver.AirParrotSpeakers (1.7 - SDK 10.7) [Click for support]
    [loaded]    com.techsmith.TACC (1.0.2 - SDK 10.8) [Click for support]
    [not loaded]    com.ups.driver.UPSVendor (1.0.0d1) [Click for support]
        /System/Library/Extensions/2.2.0/Belcarra.USBLAN_netpart.kext/Contents/Plug-Ins
    [not loaded]    com.belcarra.iokit.netpart.panther (1.6.3) [Click for support]
        /System/Library/Extensions/2.2.0/Belcarra.USBLAN_usbpart.kext/Contents/Plug-Ins
    [not loaded]    com.belcarra.iokit.usbpart.panther (1.6.3) [Click for support]
        /System/Library/Extensions/2.2.0/RemoteControl.USBLAN_usbpart.kext/Contents/Plu g-Ins
    [not loaded]    com.RemoteControl.USBLAN.panther (1.6.2) [Click for support]
        /System/Library/Extensions/ControllerMate.kext/Contents/PlugIns
    [loaded]    com.orderedbytes.driver.CMUSBDevices (4.6.0 - SDK 10.6) [Click for support]
    [not loaded]    com.orderedbytes.driver.CMUSBKeyboard (4.6.0 - SDK 10.6) [Click for support]
    [not loaded]    com.orderedbytes.driver.CMUSBPointer (4.6.0 - SDK 10.6) [Click for support]
Launch Agents: ℹ️
    [not loaded]    com.adobe.AAM.Updater-1.0.plist [Click for support]
    [loaded]    com.adobe.CS5ServiceManager.plist [Click for support]
    [running]    com.orderedbytes.ControllerMateHelper.plist [Click for support]
    [running]    com.parallels.mobile.prl_deskctl_agent.launchagent.plist [Click for support]
    [not loaded]    com.teamviewer.teamviewer.plist [Click for support]
    [not loaded]    com.teamviewer.teamviewer_desktop.plist [Click for support]
Launch Daemons: ℹ️
    [loaded]    com.adobe.fpsaud.plist [Click for support]
    [not loaded]    com.adobe.SwitchBoard.plist [Click for support]
    [loaded]    com.microsoft.office.licensing.helper.plist [Click for support]
    [running]    com.netputing.handyPrintSystemDaemon.plist [Click for support]
    [loaded]    com.oracle.java.JavaUpdateHelper.plist [Click for support]
    [running]    com.parallels.mobile.dispatcher.launchdaemon.plist [Click for support]
    [loaded]    com.parallels.mobile.kextloader.launchdaemon.plist [Click for support]
    [loaded]    com.quark.quarkupdate.plist [Click for support]
    [loaded]    com.teamviewer.Helper.plist [Click for support]
    [not loaded]    com.teamviewer.teamviewer_service.plist [Click for support]
    [not loaded]    org.virtualbox.startup.plist [Click for support]
User Launch Agents: ℹ️
    [failed]    com.acronis.monitor.plist [Click for support]
    [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.parallels.mobile.startgui.launchagent.plist [Click for support]
    [not loaded]    org.virtualbox.vboxwebsrv.plist [Click for support]
User Login Items: ℹ️
    iTunesHelper    Application  (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
    Dropbox    Application  (/Applications/Dropbox.app)
    DVDAuthorizeHelper    Application  (/Users/[redacted]/Library/Application Support/Helper/DVDAuthorizeHelper.app)
    Wondershare Helper Compact    Application  (/Users/[redacted]/Library/Application Support/Helper/Wondershare Helper Compact.app)
    USBOverdriveHelper    Application  (/Library/PreferencePanes/USB Overdrive.prefPane/Contents/Resources/USBOverdriveHelper.app)
Internet Plug-ins: ℹ️
    JavaAppletPlugin: Version: 14.9.0 - SDK 10.7 Check version
    FlashPlayer-10.6: Version: 17.0.0.134 - SDK 10.6 [Click for support]
    QuickTime Plugin: Version: 7.7.3
    Flash Player: Version: 17.0.0.134 - SDK 10.6 [Click for support]
    AdobePDFViewer: Version: 9.5.5 [Click for support]
    Default Browser: Version: 537 - SDK 10.9
    SharePointBrowserPlugin: Version: 14.4.8 - SDK 10.6 [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
    Google Earth Web Plug-in: Version: 7.1 [Click for support]
Safari Extensions: ℹ️
    1Password
    Open in Internet Explorer
    Video Converter
3rd Party Preference Panes: ℹ️
    Flash Player  [Click for support]
    Quark Update Preferences  [Click for support]
    USB Overdrive  [Click for support]
Time Machine: ℹ️
    Skip System Files: NO
    Mobile backups: OFF
    Auto backup: YES
    Volumes being backed up:
        Macintosh HD: Disk size: 499.25 GB Disk used: 308.27 GB
        Digital Media: Disk size: 999.86 GB Disk used: 725.55 GB
    Destinations:
        iMac 2TB TM Backup [Local]
        Total size: 2.00 TB
        Total number of backups: 36
        Oldest backup: 2015-03-11 08:48:55 +0000
        Last backup: 2015-03-23 10:17:51 +0000
        Size of backup disk: Too small
            Backup size 2.00 TB < (Disk used 1.03 TB X 3)
Top Processes by CPU: ℹ️
         2%    WindowServer
         1%    fontd
         1%    hidd
         0%    AppleSpell
         0%    com.apple.WebKit.Networking
Top Processes by Memory: ℹ️
    180 MB    com.apple.IconServicesAgent
    168 MB    Mail
    168 MB    Safari
    129 MB    com.apple.WebKit.WebContent
    90 MB    com.apple.WebKit.Networking
Virtual Memory Information: ℹ️
    7.36 GB    Free RAM
    3.94 GB    Active RAM
    692 MB    Inactive RAM
    892 MB    Wired RAM
    421 MB    Page-ins
    0 B    Page-outs
Diagnostics Information: ℹ️
    Mar 23, 2015, 09:47:43 PM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-23-21 4743_[redacted].crash
    Mar 23, 2015, 09:47:31 PM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-23-21 4731_[redacted].crash
    Mar 23, 2015, 09:46:19 PM    Self test - passed
    Mar 23, 2015, 08:59:14 PM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-23-20 5914_[redacted].crash
    Mar 23, 2015, 06:06:37 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-23-06 0637_[redacted].crash
    Mar 23, 2015, 06:06:36 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-23-06 0636_[redacted].crash
    Mar 22, 2015, 07:18:59 PM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-19 1859_[redacted].crash
    Mar 22, 2015, 07:09:35 PM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-19 0935_[redacted].crash
    Mar 22, 2015, 08:32:46 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-08 3246_[redacted].crash
    Mar 22, 2015, 08:32:35 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-08 3235_[redacted].crash
    Mar 22, 2015, 07:33:06 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-07 3306_[redacted].crash
    Mar 22, 2015, 07:33:05 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-07 3305_[redacted].crash
    Mar 22, 2015, 07:32:55 AM    /Library/Logs/DiagnosticReports/com.netputing.handyPrintProDaemon_2015-03-22-07 3255_[redacted].crash
Anyway, I'm gonna try the whole reset of my files and folders again and leave it a lot longer this time and see what happens.
Joe.
PS. Thanks again for all your help!

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