The class path for the compiler cannot be set by StandartFileManager.setLocation(CLASS_PATH, ...) method. I reproduce the failure under JDK b82. Please see an example below:
===Compiler.java===
import java.util.Collections;
import javax.tools.JavaCompilerTool;
import static javax.tools.JavaCompilerTool.*;
import javax.tools.JavaFileObject;
import javax.tools.StandardJavaFileManager;
import javax.tools.StandardJavaFileManager.StandardLocation;
import javax.tools.ToolProvider;

public class Compiler {
    
    public static void main(String[] argv) {
    	JavaCompilerTool compiler = 
    	    	ToolProvider.getSystemJavaCompilerTool();
        StandardJavaFileManager fileManager = 
    	    	compiler.getStandardFileManager(null);
        fileManager.setLocation(StandardLocation.CLASS_PATH,
               Collections.singleton(
    	       new File("classes/")));
        Iterable<? extends JavaFileObject> compilationUnits =
               fileManager.getJavaFileObjectsFromStrings(
    	       Collections.singleton("B.java"));
        compiler.getTask(null, fileManager, null, null, null, 
    	    	compilationUnits).run();
    	
    }    
}
====
====B.java (in the same directory as Compiler.java===
public class  B { { new A(); } }
====
====A.java (in the 'classes' directory===
public class A {}
====
====run.sh===
JDK=/java/re/jdk/6.0/latest/binaries/solaris-sparc
echo Compile Compiler.java...
$JDK/bin/javac Compiler.java
echo Invoke Compiler...
$JDK/bin/java Compiler
echo Set classpath externally and invoke compiler again...
$JDK/bin/java -cp classes:. Compiler
====
Results:
---
ag153348@oink$ . run.sh
Compile Compiler.java...
Invoke Compiler...
B.java:1: cannot find symbol
symbol  : class A
location: class B
public class  B { { new A(); } }
                        ^
1 error
Set classpath externally and invoke compiler again...
ag153348@oink$
---
It seems that the class path passed to the JavaCompilerTool via option "-cp" works fine. Currently, we use this way as a workaround.