After crash/reboot, how do get apple mail to stop pulling in old/deleted mail?

This has happend so many times, it's getting frustrating.
Finder or another program freezes, I force quit and the mac freezes.
I restart, open apple mail and it startes pulling in every piece of mails sitting on the mail server.
It's happened too many times and I end up having to delete thousands of emails.
Any idea why and how I can stop this from happening?
Thanks
497secrets

Hi Diane,
OK, i did the reindex... Hoping that does the trick.
Answering your questions:
free space: 194gb
activity monitor:
mdworker seems to be the user between 26% & 57% bouncing all over the place.
page in 2.06 gb
outs 0
Ram 9GB
EtreCheck:
Hardware Information:
    Mac Pro
    Mac Pro - model: MacPro1,1
    2 2.66 GHz Dual-Core Intel Xeon CPUs: 4 cores
    9 GB RAM
Video Information:
    NVIDIA GeForce 7300 GT - VRAM: 256 MB
System Software:
    Mac OS X 10.7.5 (11G63) - Uptime: 0 days 4:58:47
Disk Information:
    Hitachi HDE721010SLA330 disk1 : (1 TB)
        disk1s1 (disk1s1) <not mounted>: 209.7 MB
        1T-SU (disk1s2) / [Startup]: 499.67 GB (194.59 GB free)
        Recovery HD (disk1s3) <not mounted>: 650 MB
        ACTIVE JOBS (disk1s4) /Volumes/ACTIVE JOBS: 249.84 GB (196.59 GB free)
        TBD2 (disk1s5) /Volumes/TBD2: 249.05 GB (247.48 GB free)
        Recovery HD (disk1s6) <not mounted>: 650 MB
    WDC WD1001FALS-42K1B0 disk0 : (1 TB)
        disk0s1 (disk0s1) <not mounted>: 209.7 MB
        D2-T1-P1-SU2 (disk0s2) /Volumes/D2-T1-P1-SU2: 333.4 GB (326.1 GB free)
        D2-T1-P2 (disk0s3) /Volumes/D2-T1-P2: 333.4 GB (327.21 GB free)
        D2-T1-P3 (disk0s4) /Volumes/D2-T1-P3: 332.79 GB (159.23 GB free)
USB Information:
    Mitsumi Electric Hub in Apple Extended USB Keyboard
        Kensington Kensington USB/PS2 Trackball
        Mitsumi Electric Apple Extended USB Keyboard
    LG Electronics Inc. USB Monitor
    Apple Inc. Bluetooth USB Host Controller
    Seagate  Desktop          2 TB
        disk2s1 (disk2s1) <not mounted>: 209.7 MB
        2T-backup (disk2s2) /Volumes/2T-backup: 498.37 GB (496.44 GB free)
        2T-TimeMachine (disk2s3) /Volumes/2T-TimeMachine: 1.5 TB (833.4 GB free)
    EPSON USB Printer
    Hewlett-Packard OfficeJet 6100 Series
Thunderbolt Information:
Configuration files:
    /etc/hosts - Count: 21
Gatekeeper:
    Anywhere
Kernel Extensions:
    [kext loaded]    com.bresink.driver.BRESINKx86Monitoring (9.0) Support
    [kext loaded]    com.hzsystems.terminus.driver (4) Support
    [not loaded]    com.kensington.mouseworks.driver.ADBID32Mouse (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.ADBID32MouseX1 (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.ADBID4Mouse (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.ADBID4MouseX1 (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.KMWBluetoothHIDMouse (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.KMWBluetoothOldHIDMouse (3.0) Support
    [kext loaded]    com.kensington.mouseworks.driver.KMWUSBHIDMouse (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.USBMouseX1 (3.0) Support
    [kext loaded]    com.kensington.mouseworks.driver.VirtualMouse (3.0) Support
    [not loaded]    com.kensington.mouseworks.driver.VirtualMouseX1 (3.0) Support
    [kext loaded]    com.kensington.mouseworks.iokit.KensingtonMouseDriver (3.0) Support
    [not loaded]    com.kensington.mouseworks.iokit.KensingtonMouseDriverX1 (3.0) Support
    [not loaded]    com.olympus.DSSBlockCommandsDevice (2.3.0) Support
    [not loaded]    com.roxio.BluRaySupport (1.1.6) Support
    [not loaded]    com.roxio.TDIXController (2.0) Support
    [kext loaded]    net.telestream.driver.TelestreamAudio (1.1.0 - SDK 10.8) Support
Startup Items:
    ChmodBPF: Path: /Library/StartupItems/ChmodBPF
Launch Daemons:
    [loaded]    com.adobe.fpsaud.plist Support
    [loaded]    com.adobe.SwitchBoard.plist Support
    [running]    com.app4mac.CheckUpAgent.plist Support
    [loaded]    com.bresink.system.securityagent3.plist Support
    [running]    com.crashplan.engine.plist Support
    [loaded]    com.macpaw.CleanMyMac2.Agent.plist Support
    [loaded]    com.marketcircle.daylite.accessd.plist Support
    [loaded]    com.marketcircle.daylite.attachmentd.plist Support
    [loaded]    com.marketcircle.daylite.backupd.plist Support
    [running]    com.marketcircle.daylite.cardcald.plist Support
    [running]    com.marketcircle.daylite.portsd.plist Support
    [loaded]    com.marketcircle.daylite.staged.plist Support
    [loaded]    com.marketcircle.daylite.touchd.plist Support
    [loaded]    com.microsoft.office.licensing.helper.plist Support
    [loaded]    com.oracle.java.Helper-Tool.plist Support
    [loaded]    com.oracle.java.JavaUpdateHelper.plist Support
    [loaded]    com.quark.quarkupdate.plist Support
    [running]    com.starfield.backupservice.plist Support
Launch Agents:
    [not loaded]    com.adobe.AAM.Updater-1.0.plist Support
    [loaded]    com.adobe.CS5ServiceManager.plist Support
    [running]    com.extensis.FMCore.plist Support
    [loaded]    com.oracle.java.Java-Updater.plist Support
User Launch Agents:
    [loaded]    com.adobe.AAM.Updater-1.0.plist Support
    [loaded]    com.citrixonline.GoToMeeting.G2MUpdate.plist Support
    [loaded]    com.google.keystone.agent.plist Support
    [loaded]    com.macpaw.CleanMyMac2Helper.diskSpaceWatcher.plist Support
    [loaded]    com.macpaw.CleanMyMac2Helper.scheduledScan.plist Support
    [loaded]    com.macpaw.CleanMyMac2Helper.trashWatcher.plist Support
    [running]    ws.agile.1PasswordAgent.plist Support
User Login Items:
    iTunesHelper
    WorkspaceUpdate
    Dropbox
    CrashPlan menu bar
    MacLWSLauncher
    Alfred 2
    CheckUpAlert
    TransmitMenu
    Device Detector
    Default Folder X Helper
    Suitcase Fusion 5
    Admin
    Android File Transfer Agent
    MouseWorks Background
Internet Plug-ins:
    JavaAppletPlugin: Version: Java 7 Update 55 Check version
    FlashPlayer-10.6: Version: 13.0.0.214 - SDK 10.6 Support
    QuickTime Plugin: Version: 7.7.1
    AdobePDFViewerNPAPI: Version: 10.1.7 Support
    Flash Player: Version: 13.0.0.214 - SDK 10.6 Support
    AdobePDFViewer: Version: 10.1.7 Support
    SharePointBrowserPlugin: Version: 14.1.3 - SDK 10.6 Support
    iPhotoPhotocast: Version: 7.0 - SDK 10.8
Safari Extensions:
    Searchme: Version: 1.3
    Ebay Shopping Assistant: Version: 1.1
    Slick Savings: Version: 2.0
    Amazon Shopping Assistant: Version: 1.1
    1Password: Version: 3.9.20
    GoPhoto.it V9.0: Version: 1.222
Audio Plug-ins:
    iSightAudio: Version: 7.7.1 - SDK 10.7
    InstantOn: Version: 7.1.2 - SDK 10.8 Support
iTunes Plug-ins:
    Quartz Composer Visualizer: Version: 1.3 - SDK 10.7
User Internet Plug-ins:
    WbeTools64_14: Version: 1.0.23.53 © 2013 - SDK 10.6 Support
    WebEx64: Version: 1.0 - SDK 10.6 Support
    CitrixOnlineWebDeploymentPlugin: Version: 1.0.105 Support
    Google Earth Web Plug-in: Version: 7.1 Support
    fileEditTool64_15: Version: 1.0.35.65 © 2013 - SDK 10.6 Support
    ZoomUsPlugIn: Version: 1.0 - SDK 10.8 Support
3rd Party Preference Panes:
    Default Folder X  Support
    Flash Player  Support
    Growl  Support
    Java  Support
    Kensington MouseWorks  Support
    Quark Update Preferences  Support
Time Machine:
    Time Machine not configured!
Top Processes by CPU:
        17%    WebProcess
         5%    Safari
         4%    JavaApplicationStub
         2%    WindowServer
         1%    activitymonitord
Top Processes by Memory:
    839 MB    firefox
    415 MB    mds
    221 MB    JavaApplicationStub
    194 MB    WindowServer
    184 MB    Mail
Virtual Memory Information:
    4.30 GB    Free RAM
    2.98 GB    Active RAM
    1.06 GB    Inactive RAM
    666 MB    Wired RAM
    2.07 GB    Page-ins
    0 B    Page-outs
Please let me know what you see or think.
Thanks for all your help
497secrets

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