I am also facing the same issue.
Details:
Scilab version "5.1.0.1234437515"
JAVA_HOME : /usr/lib/jvm/java-1.5.0-sun/
SCI : /usr/share/scilab/
SCIBIN : /usr/bin/scilab-bin
PATH : 
/usr/share/scilab/:/usr/share/scilab//bin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH : 
/usr/lib/scilab/:/usr/lib64/scilab/:/usr/lib/jvm/java-1.5.0-sun//jre/lib/amd64/:/usr/lib/jvm/java-1.5.0-sun//jre/lib/amd64/server/:/usr/lib/jvm/java-1.5.0-sun//jre/lib/amd64/native_threads/:
DOCBOOK : 
Error in the creation of the Java VM: JNI version error
Scilab cannot open JVM library.

I have not tried it with Java6 JRE. But I would like to avoid it because of 
some other dependencies. 
Any help on this will be appreciated.
Thanks.

-- 
scilab doesn't start: JNI version error
https://bugs.launchpad.net/bugs/382342
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