My macbook slows down after using external HDD

When I use an external drive via usb, my computer really slows down giving me no choice except reboot.
I watched memory usage with activity monitor. Free memory decreases by time and inactive memory increases with the same amount and others don't change much. If I continue using -esp. reading-, free memory comes below to 100MB and then increases a bit -I think it starts paging =other applications' memories= to system disk-, then continues to decrease. Closing the application -that use the external- do not relese memory from inactive to free but ejecting the external does. After unplugging and trying to use the other applications, I face very sluggish performance so that rebooting becomes a better-fast choice. Both NTFS and FAT partitions produce the same result and I don't have any other partition.
If I try to re-read the same file after the external drive stops spinning (sleeps), it does not start spinning but trying to read another file makes it start spining. This makes me think about some -overdone- caching problem, but don't know what causes it and how to turn it off (Tuxero's caching is already disabled in the preferences, although I think it is only for writing only).
I made some research and found nothing specific; they tell to reinstall the os or format the drive -to HFS+ -. What is causing this?
Note: All of my drives are in Spotlight's exclusion (privacy) list and using another usb slot did not change a thing.
My EtreCheck is:
EtreCheck version: 1.9.11 (43) - report generated June 15, 2014
Hardware Information:
    MacBook Pro (13-inch, Mid 2009)
    MacBook Pro - model: MacBookPro5,5
    1 2.26 GHz Intel Core 2 Duo CPU: 2 cores
    4 GB RAM
Video Information:
    NVIDIA GeForce 9400M - VRAM: 256 MB
System Software:
    OS X 10.8.3 (12D78) - Uptime: 0 days 1:4:54
Disk Information:
    Hitachi HTS5450 disk0 : (160.04 GB)
        disk0s1 (disk0s1) <not mounted>: 209.7 MB
        Macintosh HD (disk0s2) / [Startup]: 94.62 GB (48.81 GB free)
        Recovery HD (disk0s3) <not mounted>: 650 MB
        BOOTCAMP (disk0s4) /Volumes/BOOTCAMP: 64.57 GB (44.49 GB free)
    HL-DT-ST DVDRW GS23N
USB Information:
    Apple Inc. Built-in iSight
    JMicron Storage 500.11 GB
        BKPFAT (disk1s1) /Volumes/BKPFAT: 443.2 GB (25.08 GB free)
        BKPNTFS (disk1s2) <not mounted>: 56.9 GB
    Apple Internal Memory Card Reader
    Apple Inc. Apple Internal Keyboard / Trackpad
    Apple Computer, Inc. IR Receiver
    Apple Inc. BRCM2046 Hub
        Apple Inc. Bluetooth USB Host Controller
Configuration files:
    /etc/hosts - Count: 1
Gatekeeper:
    Anywhere
Startup Items:
    TuxeraNTFSUnmountHelper: Path: /Library/StartupItems/TuxeraNTFSUnmountHelper
Launch Daemons:
    [loaded]    com.adobe.fpsaud.plist Support
    [loaded]    com.barebones.authd.plist Support
    [loaded]    com.barebones.textwrangler.plist Support
    [loaded]    com.google.keystone.daemon.plist Support
    [loaded]    com.oracle.java.Helper-Tool.plist Support
    [not loaded]    de.jinx.SmartSleepDaemon.plist Support
    [loaded]    org.macosforge.xquartz.privileged_startx.plist Support
Launch Agents:
    [loaded]    com.google.keystone.agent.plist Support
    [loaded]    com.oracle.java.Java-Updater.plist Support
    [loaded]    org.macosforge.xquartz.startx.plist Support
User Login Items:
    GrowlHelperApp
    Google Drive
    witchdaemon
    BetterTouchTool
Internet Plug-ins:
    JavaAppletPlugin: Version: Java 8 Update 05 Check version
    FlashPlayer-10.6: Version: 12.0.0.38 - SDK 10.6 Support
    QuickTime Plugin: Version: 7.7.1
    Flash Player: Version: 12.0.0.38 - SDK 10.6 Outdated! Update
    o1dbrowserplugin: Version: 5.4.2.18903 Support
    googletalkbrowserplugin: Version: 5.4.2.18903 Support
    Silverlight: Version: 5.1.30317.0 - SDK 10.6 Support
    Unity Web Player: Version: UnityPlayer version 4.1.5f1 Support
    iPhotoPhotocast: Version: 7.0
Safari Extensions:
    Bing Highlights: Version: 1.0.20
    ClickToFlash: Version: 2.5.1
Audio Plug-ins:
    AirPlay: Version: 1.7 - SDK 10.8
    iSightAudio: Version: 7.7.1 - SDK 10.8
iTunes Plug-ins:
    Quartz Composer Visualizer: Version: 1.4 - SDK 10.8
3rd Party Preference Panes:
    Flash Player Support
    FUSE for OS X (OSXFUSE) Support
    GamePadCompanionPrefPanel Support
    Growl Support
    Java Support
    MenuMeters Support
    SmartSleep Support
    Tuxera NTFS Support
    Witch Support
Time Machine:
    Time Machine not configured!
Top Processes by CPU:
        25% firefox
         4% activitymonitord
         4% WindowServer
         1% hidd
         1% BetterTouchTool
Top Processes by Memory:
    254 MB firefox
    111 MB Google Chrome
    66 MB   Sublime Text
    61 MB   mds
    59 MB   Google Chrome Helper
Virtual Memory Information:
    1.72 GB Free RAM
    1.21 GB Active RAM
    416 MB Inactive RAM
    425 MB Wired RAM
    378 MB Page-ins
    0 B Page-outs

Thread continues as an OSX discussion here, please do not reply this.

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On Thu, 22 Feb 2001 03:19:12 -0800 (PST), Freek wrote:
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===========================================================================
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orks Research Partner National Instruments Alliance Member
Christopher Dubea Phone: (504) 847-2280
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