Thanks for posting this Lee. I've fixed the problem in CVS (renamed back to software.jar) so it should work for the next release. Note that you can just click on the JAR and open it with Java to invoke the installer directly. For the next release, it might be nice to offer this installer via Java Web Start.
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As far as the installation progress – I've seen that too. Sounds like a bug in MyJavaPack to me. 😉