Works for me. Here was my test:
I created a clean VM of Windows 7 64-bit with nothing else of significance installed. I then fully updated it (took several tries to get all the patches.)
I then downloaded BibleDesktopSetup.exe, for the latest release, aka 1.6. Not the nightly build.
I ran BD, downloaded the version of Java that it provided, installed the KJV and created a search index and went to "Tools > Options" and then without making any changes, clicked on apply (this creates %APPDATA%/JSword/desktop.properties).
I then edited %APPDATA%\JSword\desktop.properties and changed
This adds an extra tab to Help > About that will show the system properties. With this I can see the version of Java that is actually run.
I then downloaded and installed the 64-bit version of Java 7 and uninstalled the version that BD downloaded.
I found no way to run BD using BibleDesktop.exe that would find a 64-bit JRE. It always insisted on downloading Java 6. And within the Java control panel I unchecked all the available versions of Java, but this seems to only affect the browser plugin, not what was actually used by BD.
So, I created a bat file to run the java of my choice by doing the following:
I created a folder named BD on my desktop. I then copied all the jar files from c:\Program Files (x86)\CrossWire\BibleDesktop into that folder.
I then created BD.bat in that folder with the content (on a single line):
"C:\Program Files\Java\jre7\bin\javaw.exe" -classpath "bibledesktop-1.6.jar;commons-codec-1.3.jar;commons-httpclient-3.1.jar;commons-logging-1.1.1.jar;commons-net-1.4.1.jar;javatar-2.5.jar;jdom-1.0.jar;jlfgr-1_0.jar;jsword-1.6.jar;jsword-common-1.6.jar;jsword-common-aqua-1.0.6.jar;jsword-common-swing-1.6.jar;lucene-analyzers-2.3.2.jar;lucene-core-2.3.2.jar;lucene-snowball-2.3.2.jar" org.crosswire.bibledesktop.desktop.Desktop
You can change the path of the executable to match your installation.
I then ran BD and had no problems.
Can you do the same for the latest stable release and let me know the outcome.
If it works for you, but 1.6.1beta does not, then we have a problem with the nightly build.