There are quite a few differences between the Eclipse environment and a jar file. In order to answer your question, we will need to know what your error messages you might be getting.
Common problem: file locations may not work because the OS file system does not apply to the inside of a jar. In this case, URL's are a better way to identify the resource file. There are also ways in which specifying the location of the resource can go awry, pertaining to how the relative vs absolute addressing is used. Some people also run into the mark/reset error when attempting to load a resource into an InputStream.
However, you are saying that the data IS getting loaded properly, but only the SourceDataLine is not working? I haven't run into those sorts of problems and I use Eclipse to develop programs with sound output frequently. Could you show some code, and let us know the OS environment? (For example, with some flavors of Linux, there can be contention problems over the output sound line.)
Also, without seeing anything, it is entirely possible that you have not set up the errors/exceptions to tell you if the input is failing in the jar form, and the output exists and consists of silence.