Behaviour you are describing is different in my case. After launch of app the workspace is the same like just after install. Any custom change is not stored. It is strange, but probably relative only to my OS. Datails are below:
apple.awt.showGrowBox true
apple.awt.window.position.forceSafeCreation true
apple.laf.useScreenMenuBar true
awt.dnd.drag.threshold 5
awt.toolkit sun.awt.windows.WToolkit
com.apple.macos.smallTabs true
com.apple.macos.useScreenMenuBar true
com.apple.mrj.application.apple.menu.about.name Author
com.oxygenxml.app.descriptor ro.sync.exml.AuthorFrameDescriptor
com.oxygenxml.editor.home.url file:/C:/Program%20Files/Oxygen%20XML%20Author%2010/
com.oxygenxml.editor.lib.dir C:\Program Files\Oxygen XML Author 10\lib
com.oxygenxml.editor.plugins.dir C:\Program Files\Oxygen XML Author 10\plugins
com.oxygenxml.is.eclipse.plugin false
com.oxygenxml.language English
exe4j.consoleCodepage cp0
exe4j.isInstall4j true
exe4j.launchName C:\Program Files\Oxygen XML Author 10\author.exe
exe4j.moduleName C:\Program Files\Oxygen XML Author 10\author.exe
exe4j.semaphoreName c:_program files_oxygen xml author 10_author.exe0
exe4j.tempDir
exe4j.unextractedPosition 0
file.encoding Cp1250
file.encoding.pkg sun.io
file.separator \
install4j.appDir C:\Program Files\Oxygen XML Author 10\
install4j.exeDir C:\Program Files\Oxygen XML Author 10\
java.awt.graphicsenv sun.awt.Win32GraphicsEnvironment
java.awt.printerjob sun.awt.windows.WPrinterJob
java.class.path C:\Program Files\Oxygen XML Author 10\.install4j\i4jruntime.jar;C:\Program Files\Oxygen XML Author 10\.\lib\author.jar;
java.class.version 50.0
java.endorsed.dirs c:\program files\oxygen xml author 10\jre\lib\endorsed
java.ext.dirs c:\program files\oxygen xml author 10\jre\lib\ext;C:\Windows\Sun\Java\lib\ext
java.home c:\program files\oxygen xml author 10\jre
java.io.tmpdir C:\Users\J89C0~1.VOL\AppData\Local\Temp\
java.library.path C:\Program Files\Oxygen XML Author 10;.;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program Files\Common Files\Roxio Shared\DLLShared\;C:\Program Files\Common Files\Roxio Shared\10.0\DLLShared\;C:\Program Files\TortoiseSVN\bin;C:\Program Files\QuickTime\QTSystem\;c:\program files\oxygen xml author 10\jre\bin
java.runtime.name Java(TM) SE Runtime Environment
java.runtime.version 1.6.0_11-b03
java.specification.name Java Platform API Specification
java.specification.vendor Sun Microsystems Inc.
java.specification.version 1.6
java.vendor Sun Microsystems Inc.
java.vendor.url
http://java.sun.com/
java.vendor.url.bug
http://java.sun.com/cgi-bin/bugreport.cgi
java.version 1.6.0_11
java.vm.info mixed mode
java.vm.name Java HotSpot(TM) Client VM
java.vm.specification.name Java Virtual Machine Specification
java.vm.specification.vendor Sun Microsystems Inc.
java.vm.specification.version 1.0
java.vm.vendor Sun Microsystems Inc.
java.vm.version 11.0-b16
javax.xml.parsers.DocumentBuilderFactory org.apache.xerces.jaxp.DocumentBuilderFactoryImpl
javax.xml.parsers.SAXParserFactory org.apache.xerces.jaxp.SAXParserFactoryImpl
line.separator \r\n
org.apache.xerces.xni.parser.XMLParserConfiguration org.apache.xerces.parsers.XIncludeAwareParserConfiguration
org.eclipse.emf.ecore.EPackage.Registry.INSTANCE org.eclipse.emf.ecore.impl.EPackageRegistryImpl
org.xml.sax.driver org.apache.xerces.parsers.SAXParser
os.arch x86
os.name Windows Vista
os.version 6.0
path.separator ;
sun.arch.data.model 32
sun.boot.class.path c:\program files\oxygen xml author 10\jre\lib\resources.jar;c:\program files\oxygen xml author 10\jre\lib\rt.jar;c:\program files\oxygen xml author 10\jre\lib\sunrsasign.jar;c:\program files\oxygen xml author 10\jre\lib\jsse.jar;c:\program files\oxygen xml author 10\jre\lib\jce.jar;c:\program files\oxygen xml author 10\jre\lib\charsets.jar;c:\program files\oxygen xml author 10\jre\classes
sun.boot.library.path c:\program files\oxygen xml author 10\jre\bin
sun.cpu.endian little
sun.cpu.isalist pentium_pro+mmx pentium_pro pentium+mmx pentium i486 i386 i86
sun.desktop windows
sun.io.unicode.encoding UnicodeLittle
sun.java2d.noddraw true
sun.jnu.encoding Cp1250
sun.management.compiler HotSpot Client Compiler
sun.os.patch.level Service Pack 1
sun.swing.enableImprovedDragGesture true
user.country CZ
user.dir C:\Program Files\Oxygen XML Author 10
user.home C:\Users\honyk
user.language cs
user.name honyk
user.timezone Europe/Prague
user.variant