If path for signing jar look like c:\aaa\..\bbb\my.jar and not destDir nor destFile are defined sign procedure finish with error:
jzfile = 43261776,
total = 5, 
name = c:\bbb\my.jar\com.borland.orbit_8.2.3.v20101012-1621.jar,
i = 1, 
message = couldn't read LOC header
at java.util.zip.ZipFile$3.nextElement(ZipFile.java:429)
at java.util.zip.ZipFile$3.nextElement(ZipFile.java:415)
at sun.security.tools.JarSigner.getManifestFile(JarSigner.java:1449)
at sun.security.tools.JarSigner.signJar(JarSigner.java:836)
at sun.security.tools.JarSigner.run(JarSigner.java:194)
at sun.security.tools.JarSigner.main(JarSigner.java:75)

It happened because in SignJar.signOneJar(File jarSource, File jarTarget) 
jarSource = c:\aaa\..\bbb\my.jar
jarTarget = c:\bbb\my.jar
It points on the same file but !jarSource.equals(targetFile)
So code add "-signedjar" argument in command call but should not.

SignJar.signOneJar:377
        //DO NOT SET THE -signedjar OPTION if source==dest
        //unless you like fielding hotspot crash reports
        if (!jarSource.equals(targetFile)) {
            addValue(cmd, "-signedjar");
            addValue(cmd, targetFile.getPath());
        }