Do You Know Which Jar Command You Are Using?
If you use both the Sun J2SE SDK and a full installation of GCC 3.2.x or later on the same machine, then there is a chance that when you issue the jar command from a command prompt, the wrong jar command is used.
Depending on how your PATH is setup, either the jar from GCC is always being run or the one from the JDK is always being run.
I found out that I've been using the GNU version in a Cygwin environment when I tried to do a jar -u and received an error message:
jar: `-u' mode unimplemented
The two versions are mostly compatible with the exception of the -u and the -i switches. The GNU version runs a lot faster.