Do you use openjdk or sun jdk? I will try to reproduce. Problem might be in 
freemarker as it should load logger from jdk in 
freemarker.log.Log4JLoggerFactory.getLogger(Log4JLoggerFactory.java:65)
freemarker.log.Logger.getLogger(Logger.java:255)
freemarker.template.utility.SecurityUtilities.<clinit>(SecurityUtilities.java:67)
I will look at freemarker sources.

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Update NetBeans to 6.5
https://bugs.launchpad.net/bugs/251173
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