When javac is invoked using jsr199, such as
 
javax.tools.JavaCompiler javac = ToolProvider.getSystemJavaCompiler();
 DiagnosticCollector<JavaFileObject> diagnostics =
           new DiagnosticCollector<JavaFileObject>();
 StandardJavaFileManager stdFileManager =
           javac.getStandardFileManager(diagnostics, null, null);
 stdFileManager.setLocation(StandardLocation.CLASS_PATH, cpath);
 etc.

If cpath is a jar file, the jar files specified in its manifest Class-Path attribute are not included in the classpath of the Java Compilation, resulting in errors.