I think that the path is not recognized in your case,try to create package in Java project,insert there your VBScript(for example the name of the package is "vbnet"),and for instance your class name where you wanna execute the vbscript is Exec,so you should specify the follofing:
Runtime.getRuntime().exec("wscript \"+"""+Exec.class.getRecourse("/vbnet/script.vbs")+""");
Then your script will be found and will be launched with Runtime