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I have had the same problem with Zimbra Desktop since at least Fedora 22. I just managed to work around it by doing the following. Note: I do not claim that my solution is correct or that anyone else should follow it.

1. Inside the newly-downloaded/extracted directory containing the Zimbra app, open the script install.pl in a text editor and remove the "exit;" from the line: "else { print "Java SE Runtime Environment (JRE) not found. Please install JRE 1.6 or later.\n"; exit;}". This will prevent the installation from exiting, if the installer does not detect the appropriate java version in your system.
2. Install the app by running the script, as explained in the Zimbra documentation.
3. Run the user-install.pl according to the documentation.
4. If you have followed beduine's answer above, it means that you will have the 32-bit JDK version in your /opt/ directory. You will need to point to this java version in the following two files: "/opt/zimbra/zdesktop/data/bin/zdesktop" and "/home/user/zdesktop/bin/zdesktop". To do this, simply comment out the line JAVA=which java and add the line JAVA="/opt/jdk_directory/jre/bin/java".
   
   You may need to install some extra packages, so it is probably better to run Zimbra from the terminal and look for missing packages-related warnings/errors.
   
   Hope this helps.