EVALUATION

The trouble here is that Jar-file does not contain any classes so the 1.6 pack200
generates a java6 compatible class, one can add a dummy class compiled with -target 5. Simple annotating JARs which are devoid of any classes should not use pack200
and instead rely on http-compression using gzip.
The above behavior and deployment strategies are described here:
http://java.sun.com/javase/6/docs/technotes/guides/deployment/deployment-guide/pack200.html

See the workaround section for more info.
                                     

WORK AROUND

add a null class as shown below compiled with -target 5.

The test script:
% cat doit
#!/bin/sh -x

echo "create a failure case"
echo "Junk" > junk
jar cvf foo.jar junk
/usr/jdk/instances/jdk1.6.0/bin/pack200 foo.jar.pack.gz foo.jar
/usr/jdk/instances/jdk1.5.0/bin/unpack200 foo.jar.pack.gz bar.jar


echo "demonstrate how to fix this"
printf "public class Foo{}" > Foo.java
/usr/jdk/instances/jdk1.6.0/bin/javac -target 5 Foo.java
jar uvf foo.jar Foo.class

rm -f bar.jar
/usr/jdk/instances/jdk1.6.0/bin/pack200 foo.jar.pack.gz foo.jar
/usr/jdk/instances/jdk1.5.0/bin/unpack200 foo.jar.pack.gz bar.jar

if [ -f bar.jar ]; then
  printf "It worked\n"
fi

% ./doit
+ echo create a failure case 
create a failure case
+ echo Junk 
+ jar cvf foo.jar junk 
added manifest
adding: junk(in = 5) (out= 7)(deflated -40%)
+ /usr/jdk/instances/jdk1.6.0/bin/pack200 foo.jar.pack.gz foo.jar 
+ /usr/jdk/instances/jdk1.5.0/bin/unpack200 foo.jar.pack.gz bar.jar 
Corrupted pack file: magic/ver = CAFED00D/160.1 should be CAFED00D/150.7

+ echo demonstrate how to fix this 
demonstrate how to fix this
+ printf public class Foo{} 
+ /usr/jdk/instances/jdk1.6.0/bin/javac -target 5 Foo.java 
+ jar uvf foo.jar Foo.class 
adding: Foo.class(in = 180) (out= 152)(deflated 15%)
+ rm -f bar.jar 
+ /usr/jdk/instances/jdk1.6.0/bin/pack200 foo.jar.pack.gz foo.jar 
+ /usr/jdk/instances/jdk1.5.0/bin/unpack200 foo.jar.pack.gz bar.jar 
+ [ -f bar.jar ] 
+ printf It worked\n 
It worked