Black Square on Boot Screen after last update

Hi everybody, I made the last security update of OSX on May 25th, (osx 10.9.3), and iTunes 11.2.2 on June 10th.
I do not use to reboot so much the computer, but I do that every 10 or 20 days. After one of those updates, I got these screen while booting up the computer:
As you can see, there is a black square, with the cursor over it. I can move the cursor and the computer seems to start without problems (actually faster) but showing that square. The other difference is also that now I cannot see the usual spinner under the apple logo.
I do not have any kind of boot camp or other OS installed. I have only changed the HD for an SSD one, but this was at november of last year, and everything has worked without problems until this date.
If anybody can give an idea on how to solve it, or if I am the only one who is havving this issue, please, post it here.
Thank you very much

So here it is:
EtreCheck version: 1.9.11 (43) - report generated 15 de junio de 2014 20:31:23 GMT+2
Hardware Information:
          MacBook Pro (13-inch, Late 2011)
          MacBook Pro - model: MacBookPro8,1
          1 2.4 GHz Intel Core i5 CPU: 2 cores
          4 GB RAM
Video Information:
          Intel HD Graphics 3000 - VRAM: 384 MB
System Software:
          OS X 10.9.3 (13D65) - Uptime: 0 days 1:27:21
Disk Information:
          KINGSTON SH103S3120G disk0 : (120,03 GB)
                    EFI (disk0s1) <not mounted>: 209,7 MB
                    MacintoshHD (disk0s2) / [Startup]: 119,17 GB (19,14 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          MATSHITADVD-R   UJ-8A8
USB Information:
          Apple Computer, Inc. IR Receiver
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Inc. BRCM2070 Hub
                    Apple Inc. Bluetooth USB Host Controller
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
Configuration files:
          /etc/hosts - Count: 20
Gatekeeper:
          Anywhere
Kernel Extensions:
          [kext loaded] com.shapeservices.msm.driver.MSMFramebuffer (3.3.2 - SDK 10.6) Support
          [kext loaded] com.shapeservices.msm.driver.MSMVideoDevice (3.3.2 - SDK 10.6) Support
Startup Items:
          ChmodBPF: Path: /Library/StartupItems/ChmodBPF
          MySQLCOM: Path: /Library/StartupItems/MySQLCOM
Launch Daemons:
          [loaded] ag.shape.MSMToolHelper.plist Support
          [loaded] com.adobe.fpsaud.plist Support
          [loaded] com.adobe.SwitchBoard.plist Support
          [loaded] com.google.keystone.daemon.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] org.macosforge.xquartz.privileged_startx.plist Support
Launch Agents:
          [not loaded] com.adobe.AAM.Updater-1.0.plist Support
          [loaded] com.adobe.CS5ServiceManager.plist Support
          [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:
          iTunesHelper
          TimingHelper
          SpeechSynthesisServer
Internet Plug-ins:
          FlashPlayer-10.6: Version: 12.0.0.44 - SDK 10.6 Support
          QuickTime Plugin: Version: 7.7.3
          Flash Player: Version: 12.0.0.44 - SDK 10.6 Outdated! Update
          Default Browser: Version: 537 - SDK 10.9
          o1dbrowserplugin: Version: 5.4.2.18903 Support
          SharePointBrowserPlugin: Version: 14.0.0 Support
          googletalkbrowserplugin: Version: 5.4.2.18903 Support
          Silverlight: Version: 5.1.20913.0 - SDK 10.6 Support
          Unity Web Player: Version: UnityPlayer version 4.3.5f1 - SDK 10.6 Support
          JavaAppletPlugin: Version: Java 7 Update 55 Check version
Safari Extensions:
          AdBlock: Version: 2.7.1
          BugMeNot: Version: 1.2
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 2.0 - SDK 10.9
          AppleAVBAudio: Version: 203.2 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
iTunes Plug-ins:
          CoverVersion: Version: 2.1.6 - SDK 10.8 Support
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.9
3rd Party Preference Panes:
          Flash Player Support
          Growl Support
          Java Support
Time Machine:
          Time Machine not configured!
Top Processes by CPU:
               3%          WindowServer
               3%          eclipse
               2%          Mail
               1%          loginwindow
               0%          fontd
Top Processes by Memory:
          553 MB          eclipse
          172 MB          Safari
          100 MB          Mail
          82 MB          SourceTree
          74 MB          com.apple.quicklook.satellite
Virtual Memory Information:
          66 MB          Free RAM
          1.09 GB          Active RAM
          1.04 GB          Inactive RAM
          1020 MB          Wired RAM
          716 MB          Page-ins
          12 MB          Page-outs

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