FULL PRODUCT VERSION :
$ java -version
java version "1.6.0_15"
Java(TM) SE Runtime Environment (build 1.6.0_15-b03)
Java HotSpot(TM) Client VM (build 14.1-b02, mixed mode, sharing)

$ java -version
java version "1.7.0-ea"
Java(TM) SE Runtime Environment (build 1.7.0-ea-b73)
Java HotSpot(TM) Client VM (build 17.0-b02, mixed mode, sharing)

ADDITIONAL OS VERSION INFORMATION :
Not OS specific

A DESCRIPTION OF THE PROBLEM :
See example maven project attached to the issue:

http://jira.codehaus.org/browse/JRUBY-4057


If both jruby and jython are enabled using runtime dependencies*

pom.xml:
<dependencies>
 <dependency>
  <groupId>org.jruby</groupId>
  <artifactId>jruby</artifactId>
  <version>1.4.0RC1</version>
  <scope>runtime</scope>
 </dependency>
 <dependency>
  <groupId>org.python</groupId>
  <artifactId>jython</artifactId>
  <version>2.5.1</version>
  <scope>runtime</scope>
 </dependency>
</dependencies>

then the jar-with-dependencies assembly jar will fail to register both ScriptEngine implementations

$ mvn assembly:assembly
$ java -jar target/example-1.0-SNAPSHOT-jar-with-dependencies.jar
could not find jruby engine

whereas creating an explicit classpath works fine

$ java -classpath "jython-2.5.1.jar;jruby-1.4.0RC1.jar;target/example-1.0-SNAPSHOT.jar" example.Jsr223Example
ok

It appears the JSR223 mechanism cannot handle multiple copies of its metadata in example-1.0-SNAPSHOT-jar-with-dependencies.jar.

$ jar tvf target/example-1.0-SNAPSHOT-jar-with-dependencies.jar | grep javax.script.ScriptEngineFactory
42 Wed Sep 16 13:39:46 CDT 2009 META-INF/services/javax.script.ScriptEngineFactory
40 Sat Sep 26 13:48:04 CDT 2009 META-INF/services/javax.script.ScriptEngineFactory

    * - please note a jython-2.5.1.jar artifact is not yet available on maven central repo, will have to be installed manually

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
See description above

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
$ mvn assembly:assembly
$ java -jar target/example-1.0-SNAPSHOT-jar-with-dependencies.jar
ok
ACTUAL -
$ mvn assembly:assembly
$ java -jar target/example-1.0-SNAPSHOT-jar-with-dependencies.jar
could not find jruby engine

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
See example maven project attached to the issue:

http://jira.codehaus.org/browse/JRUBY-4057
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Workaround would be to not use the maven assembly plugin to build a jar-with-dependencies jar, which is not possible for out project.