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I created a "Java project from existing sources" and added a custom Java platform to the IDE (my own build of JDK 6U10) but any non-default platform jvm will show this (e.g. run on JDK 6 and add JDK 5 as extra) I selected this extra JVM as the Java Platform for the project and tried to run a file in the project. Both "Run File" and (once I set this as the main class) "Run Project" used the IDE's default JVM instead of the one I'd selected for the project. Since the project I was running was testing JVM differences, you can see how this could be a problem...
This works in 6.1.
Thanks for the report. There is one report describing this issue -> I will make this report duplicate of the issue report with higher priority. *** This issue has been marked as a duplicate of 142657 ***