Run this test case using JDK 6u18 or JDK 7 b77:

---%<---
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.util.Arrays;
import java.util.Collections;
import java.util.Set;
import javax.annotation.processing.AbstractProcessor;
import javax.annotation.processing.RoundEnvironment;
import javax.annotation.processing.SupportedAnnotationTypes;
import javax.annotation.processing.SupportedSourceVersion;
import javax.lang.model.SourceVersion;
import javax.lang.model.element.TypeElement;
import javax.tools.Diagnostic.Kind;
import javax.tools.FileObject;
import javax.tools.JavaCompiler;
import javax.tools.JavaCompiler.CompilationTask;
import javax.tools.StandardLocation;
import javax.tools.ToolProvider;
@SupportedAnnotationTypes("*")
@SupportedSourceVersion(SourceVersion.RELEASE_6)
public class Demo extends AbstractProcessor {
    public static void main(String[] args) throws Exception {
        File srcdir = mkdir("src");
        File destdir = mkdir("dest");
        write(srcdir, "pkg/X.java", "package pkg; class X {}");
        write(srcdir, "resources/file.txt", "hello");
        JavaCompiler javac = ToolProvider.getSystemJavaCompiler();
        System.err.println("got compiler from " + javac.getClass().getProtectionDomain().getCodeSource().getLocation());
        CompilationTask task = javac.getTask(null, null, null,
                Arrays.asList("-sourcepath", srcdir.toString(), "-d", destdir.toString()),
                Collections.singleton("pkg.X"), null);
        task.setProcessors(Collections.singleton(new Demo()));
        System.err.println("javac result with single source dir: " + task.call());
        srcdir = mkdir("src");
        File rsrcdir = mkdir("rsrc");
        write(srcdir, "pkg/X.java", "package pkg; class X {}");
        write(rsrcdir, "resources/file.txt", "hello");
        task = javac.getTask(null, null, null,
                Arrays.asList("-sourcepath", srcdir + File.pathSeparator + rsrcdir, "-d", destdir.toString()),
                Collections.singleton("pkg.X"), null);
        task.setProcessors(Collections.singleton(new Demo()));
        System.err.println("javac result with composite source path: " + task.call());
        srcdir = mkdir("src");
        write(srcdir, "pkg/X.java", "package pkg; class X {}");
        task = javac.getTask(null, null, null,
                Arrays.asList("-sourcepath", srcdir.toString(), "-d", destdir.toString()),
                Collections.singleton("pkg.X"), null);
        task.setProcessors(Collections.singleton(new Demo()));
        System.err.println("javac result when missing resource: " + task.call());
    }
    public @Override boolean process(Set<? extends TypeElement> annotations, RoundEnvironment roundEnv) {
        if (roundEnv.processingOver()) {
            return false;
        }
        try {
            FileObject resource = processingEnv.getFiler().getResource(StandardLocation.SOURCE_PATH, "resources", "file.txt");
            try {
                resource.openInputStream().close();
                processingEnv.getMessager().printMessage(Kind.NOTE, "found: " + resource.toUri());
                return true;
            } catch (IOException x) {
                processingEnv.getMessager().printMessage(Kind.ERROR, "did not find: " + resource.toUri());
                x.printStackTrace();
            }
        } catch (IOException x) {
            processingEnv.getMessager().printMessage(Kind.ERROR, "did not find resource");
            x.printStackTrace();
        }
        return false;
    }
    private static File mkdir(String name) throws IOException {
        File dir = File.createTempFile(name, "");
        if (!dir.delete()) {
            throw new IOException(dir.toString());
        }
        if (!dir.mkdir()) {
            throw new IOException(dir.toString());
        }
        dir.deleteOnExit();
        return dir;
    }
    private static File write(File dir, String path, String contents) throws IOException {
        int i = path.indexOf('/');
        if (i == -1) {
            File f = new File(dir, path);
            f.deleteOnExit();
            Writer w = new FileWriter(f);
            try {
                w.write(contents);
            } finally {
                w.close();
            }
            return f;
        } else {
            File subdir = new File(dir, path.substring(0, i));
            subdir.deleteOnExit();
            if (!subdir.mkdir()) {
                throw new IOException(subdir.toString());
            }
            return write(subdir, path.substring(i + 1), contents);
        }
    }
}
---%<---

On Ubuntu, I get:

---%<---
got compiler from file:..../jdk1.6.0_18/lib/tools.jar
Note: found: /tmp/src2920143692070020157/resources/file.txt
javac result with single source dir: true
error: did not find: /tmp/src453264489814761295/resources/file.txt
java.io.FileNotFoundException: /tmp/src453264489814761295/resources/file.txt (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:106)
        at com.sun.tools.javac.util.DefaultFileManager$RegularFileObject.openInputStream(DefaultFileManager.java:1277)
        at javax.tools.ForwardingFileObject.openInputStream(ForwardingFileObject.java:56)
        at Demo.process(Demo.java:59)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.callProcessor(JavacProcessingEnvironment.java:624)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.discoverAndRunProcs(JavacProcessingEnvironment.java:553)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.doProcessing(JavacProcessingEnvironment.java:698)
        at com.sun.tools.javac.main.JavaCompiler.processAnnotations(JavaCompiler.java:981)
        at com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:727)
        at com.sun.tools.javac.main.Main.compile(Main.java:353)
        at com.sun.tools.javac.api.JavacTaskImpl.call(JavacTaskImpl.java:115)
        at Demo.main(Demo.java:43)
1 error
javac result with composite source path: false
error: did not find: /tmp/src756707934637178516/resources/file.txt
java.io.FileNotFoundException: /tmp/src756707934637178516/resources/file.txt (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:106)
        at com.sun.tools.javac.util.DefaultFileManager$RegularFileObject.openInputStream(DefaultFileManager.java:1277)
        at javax.tools.ForwardingFileObject.openInputStream(ForwardingFileObject.java:56)
        at Demo.process(Demo.java:59)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.callProcessor(JavacProcessingEnvironment.java:624)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.discoverAndRunProcs(JavacProcessingEnvironment.java:553)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.doProcessing(JavacProcessingEnvironment.java:698)
        at com.sun.tools.javac.main.JavaCompiler.processAnnotations(JavaCompiler.java:981)
        at com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:727)
        at com.sun.tools.javac.main.Main.compile(Main.java:353)
        at com.sun.tools.javac.api.JavacTaskImpl.call(JavacTaskImpl.java:115)
        at Demo.main(Demo.java:50)
1 error
javac result when missing resource: false
---%<---

The second stack trace, from the third javac run, is expected (though the timing is odd: getResource succeeds). But the first error, from the second run, is not: resources/file.txt is present in the sourcepath passed to the compiler and ought to have been found.