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.
Specificly: 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.