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Wasn't this working before 7.1.2?
Dev build, JDK 7, Ubuntu. File > New Project, NetBeans Modules > NetBeans Platform Application. Package as > ZIP Distribution. Files > (name) > dist > (name).zip > (name) > etc > (name).conf has default_options="--branding (name) -J-Xms24m -J-Xmx64m" as expected. If you see something else, please provide complete steps to reproduce from scratch.