Method getModuleLocation(Location, String) works with StandardLocation.SYSTEM_MODULES.
But it returns null in case of StandardLocation.MODULE_PATH.
In this case compiled module is located in module path of JVM.
This was tested for JDK9 b126.

Minimal test case:

Test/src/mod1/module-info.java
module mod1{
    requires java.compiler;
}

Test/src/mod1/pack/A.java
package pack;
public class A{
    public static void main(String[] args) throws Exception{
         StandardJavaFileManager fm = ToolProvider.getSystemJavaCompiler().getStandardFileManager(null, null, null);
         fm.setLocationFromPaths(StandardLocation.MODULE_PATH, Arrays.asList(Paths.get("/Test/out")));
         JavaFileManager.Location sourceLocation = StandardLocation.MODULE_PATH;
        JavaFileManager.Location location = fm.getModuleLocation(sourceLocation, "mod2");
        System.out.println((location == null) ? "Module not found" : "Module is found");
     }
}

In Test/out there is directory 'mod2' with compiled module.
Command:
java -mp out -m mod1/pack.A


Following tests fail due to this issue:
api/javax_tools/JavaFileManager/index.html#GetModuleLocation[getModuleLocation0001]
api/javax_tools/JavaFileManager/index.html#GetModuleLocation[getModuleLocation0011]
api/javax_tools/JavaFileManager/index.html#GetModuleLocation[getModuleLocation0003]
api/javax_tools/JavaFileManager/index.html#InferModuleName[inferModuleName0001]