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I have a "Java project from existing sources". I created a custom config and set run.jvmargs via project properties and they are being ignored when I run the app. I then set them on the default config - still ignored. From enabling <debug> verbosity from ant, it looks like more properties than this are being ignored. The discovery of exactly which ones is left as an exercise for the reader. P2 because I had to drop using 6.5 for this project and switch back to 6.1. Ignoring startup properties is not acceptable and there does not appear to be a work around.
Could you please specify was exact build are you using? There were such problems, and have been fixed as issue #141454 (as have been a few more problems). If you are still able to reproduce in an up-to-date build, please attach messages.log and the output from "debug" ant output. Please note also Project Properties/Compile/Compile on Save checkbox.
build from around 7/23/08. Sorry, wasn't easy to test a newer build in this case. Sounds like you've already fixed it.
That good news. Please reopen if it happens in a new build. Thanks. *** This issue has been marked as a duplicate of 141454 ***