Matching preview only shows top half of the screen

multi monitor?

run with -d 3 from command line:
monitor config?

Laptop(lenovo T series) monitor , 1366X768.

running SikuliX: -Xmx512M -Dfile.encoding=UTF-8 -Dsikuli.FromCommandLine
-jar ./sikulix.jar -d 3 -c
[debug] init user preferences
[debug] RunTimeINIT: global init: entering as: IDE
[debug] RunTimeINIT: ScreenDevice 0 contains (0,0) --- will be used as primary
[debug] RunTimeINIT: runs as sikulix.jar in: /home/race/workspace/sikuli/Setup
[debug] RunTimeINIT: exists libs folder at: /home/race/.Sikulix/SikulixLibs_201503240850
***** show environment for IDE
user.home: /home/race
user.dir (work dir): /home/race/workspace/sikuli/Setup
user.name: race
java.io.tmpdir: /tmp
running 64Bit on Linux (3.13.0-48-generic) from a jar
java 7-64 version 1.7.0_76-b13 vm 24.76-b04 class 51.0 arch amd64
app data folder: /home/race/.Sikulix
libs folder: /home/race/.Sikulix/SikulixLibs_201503240850
executing jar: /home/race/workspace/sikuli/Setup/sikulix.jar
*** classpath dump sikulix
  0: /home/race/workspace/sikuli/Setup/sikulix.jar
*** classpath dump end
***** show environment end
[debug] RunTimeIDE: global init: leaving
[debug] RunTimeIDE: initIDEbefore: entering
[debug] RunTimeIDE: initIDEbefore: leaving
[debug] IDE: running with Locale: en_US
[debug] --- Sikuli parameters ---
[debug] 1: -d
[debug] 2: 3
[debug] 3: -c
[debug] RunTimeIDE: loadLib: libJXGrabKey.so
[debug] RunTimeIDE: ldd -r /home/race/.Sikulix/SikulixLibs_201503240850/libJXGrabKey.so
[error] LinuxSupport: : checking: might not work, has undefined symbols: libJXGrabKey.so
[debug] LinuxSupport: pthread_spin_lock:pthread_spin_unlock:pthread_spin_init:pthread_spin_destroy:
[info] HotkeyManager: add Capture Hotkey: CTRL+SHIFT 2 (50, 3)
[debug] HotkeyManager: add Capture Hotkey: CTRL+SHIFT 2 (50, 3)
[info] HotkeyManager: add Abort Hotkey: ALT+SHIFT C (67, 9)
[debug] HotkeyManager: add Abort Hotkey: ALT+SHIFT C (67, 9)
[debug] ScriptingSupport: initScriptingSupport: enter
[debug] JythonSupport: init: starting
[debug] JythonSupport: init: success
[debug] JythonSupport: ***** Jython sys.path
 0: /home/race/workspace/sikuli/Setup/Lib
 1: /home/race/workspace/sikuli/Setup/sikulix.jar/Lib
 2: __classpath__
 3: __pyclasspath__/
[debug] JythonSupport: ***** Jython sys.path end
[debug] Jython: sikuli: Sikuli: starting init
[debug] RunTimeIDE: loadLib: libVisionProxy.so
[debug] RunTimeIDE: ldd -r /home/race/.Sikulix/SikulixLibs_201503240850/libVisionProxy.so
[debug] LinuxSupport: : checking: should work: libVisionProxy.so
[debug] Mouse: init
[debug] KeyBoard: init
[debug] RunTimeIDE: wmctrl -m
[debug] RunTimeIDE: xdotool version
[debug] Jython: requested to use as default region: R[0,0 1366x768]@S(0)
[debug] Jython: sikuli: Sikuli: ending init
[debug] JythonScriptRunner: running Jython 2.7b3
[debug] ScriptingSupport: initScriptingSupport: added: jython
[debug] ScriptingSupport: initScriptingSupport: warning: org.sikuli.scriptrunner.IScriptRunner: Provider org.sikuli.scriptrunner.JRubyScriptRunner could not be instantiated
[debug] ScriptingSupport: initScriptingSupport: exit with defaultrunner: jython (py)
[debug] IDE: Adding components to window
[debug] [I18N] menuRecent
[debug] IDE: creating tabbed editor
[debug] IDE: creating message area
[debug] IDE: creating combined work window
[debug] IDE: Putting all together
[debug] restore session: /home/race/workspace/sw/raceTest.sikuli
[debug] IDE: doNew: create new tab at: -1
[debug] EditorPane: EditorPane: creating new pane (constructor)
[debug] EditorPane: loadfile: /home/race/workspace/sw/raceTest.sikuli
[debug] ImagePath: new BundlePath:
/home/race/workspace/sw/raceTest.sikuli/
[debug] EditorPane: initBeforeLoad: py
[debug] EditorPane: updateDocumentListeners from: initBeforeLoad
[debug] EditorPane: InitTab: (text/python)
[debug] SikuliEditorKit.read
[debug] Image: loaded: 1427879373427.png (file:/home/race/workspace/sw/raceTest.sikuli/1427879373427.png)
[debug] Image: cached: 1427879373427.png (3 KB) (# 1 KB 3 -- 0 % of 64 MB)
[debug] Image: reused: 1427879373427.png (file:/home/race/workspace/sw/raceTest.sikuli/1427879373427.png)
[debug] EditorPane: updateDocumentListeners from: loadFile
[info] IDE startup: 12.9 seconds
[debug] IDE startup: 12.9 seconds
[debug] ThumbButtonLabel: open Pattern Settings
[debug] ScreenUnion: capture: (0,0) 1366x768
[debug] Image: reused: 1427879373427.png (file:/home/race/workspace/sw/raceTest.sikuli/1427879373427.png)
[debug] Image: reused: 1427879373427.png (file:/home/race/workspace/sw/raceTest.sikuli/1427879373427.png)
[debug] ThumbButtonLabel: open Pattern Settings
[debug] ScreenUnion: capture: (0,0) 1366x768
[debug] Image: reused: 1427879373427.png (file:/home/race/workspace/sw/raceTest.sikuli/1427879373427.png)
[debug] Image: reused: 1427879373427.png (file:/home/race/workspace/sw/raceTest.sikuli/1427879373427.png)
[debug] IDE: doQuit requested
[debug] Sikulix: cleanUp: 0
[debug] RunTimeIDE: final cleanup
[debug] FileManager: deleteFileOrFolder:
/tmp/Sikulix

Single Monitor.

ok, thanks.

besides the fact, that you are not using the latest nightly build, I cannot see any specifics.
please upgrade and test again.

I will check on my Ubuntu later.