This bug now is reproducible in the latest Mustang beta build 59e also.

java is not working after mustang upgrade/downgrage from/to 1.3.1_X/1.4.2_X/1.5.0_X on windows.
Steps to reproduce:
- install mustang (jre1.6.0) build 65 (promoted)
- make sure "java -version" is working
- install tiger update (jre1.5.0_06) (latest promoted)
- try "java -version", it is not working
- uninstall jre1.5.0_06
- try "java -version" again, it is not working
and if you in step 5 uninstall jre1.6.0, java will be removed totaly from windows system dir (but we still have jre1.5 on the machine)
It is a regression. Everything works fine with jre1.6.0_build62
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I did further testing and it is looks worse then it was from the beginning:

This is how our Mustang behave now:

1) Upgrade from 1.3.1_X to Mustang

- on clean machine (no jre), install 1.3.1_X version
- upgrade it to Mustang (you can use any build starting from build 64 (63 working fine))
- remove 1.3.1_X version (uninstall 1.3.1_X)
- try java ("Command not found") (this is another bug, I think not related to Joe's changes)
- from IE, try "Sun Java Console" - it is not registered (this is another bug, I think not related to Joe's changes)
- now, if you try to execute javaws error coming:
Initial Java Virtual Machine Launcher
Failing reading value of registry key:Software\JavaSoft\Java Runtime Environment\CurrentVersion

Same scenario working fine with build 63

2) Upgrade from 1.4.2_X to Mustang

- on clean machine (no jre), install 1.4.2_X version
- upgrade it to Mustang (you can use any build starting from build 65 (64 working fine))
- remove 1.4.2_X version (uninstall 1.4.2_X)
- now try to execute java, it is not responding at all (javaws working fine)

Same scenario working fine with build 64

3) Upgrade from 1.5.0_X to Mustang

- on clean machine (no jre), install 1.5.0_X version
- upgrade it to Mustang (you can use any build starting from build 65 (64 working fine))
- remove 1.5.0_X version (uninstall 1.5.0_X)
- now try to execute java, it is not responding at all (javaws working fine)

Same scenario working fine with build 64