| | Same here...
I've been experiencing the same issues trying to package certain BlackBerry projects using Eclipse (4.5) and the BB IDE for Eclipse (1.1beta).
If a project doesn't have external libraries, things work okay for me, but my biggest project with external libraries causes this error while packaging the project.
As a workaround, I copied the failed command (display in the packaging console window) into a command prompt from the project's directory and it worked fine.
My system's path is set properly to pick up jar.exe from the installed JDK's bin directory and it's obvious that something in Eclipse isn't picking up the right paths and I am unsure where to set them myself.