Don't mess with the library path! Eclipse builds it itself!
Instead, go into the library settings for your projects and, for each jar/etc that requires a native library, expand it in the Libraries tab. In the tree view there, each library has items for source/javadoc and native library locations.
Specifically: select Project, right click -> Properties / Java Build Path / Libraries tab, select a .jar, expand it, select Native library location, click Edit, folder chooser dialog will appear)
Messing with the library path on the command line should be your last ditch effort, because you might break something that is already properly set by eclipse.