batch goto :eof not working when called from java

I have a batch file roughly with the following code:

@echo off
(
    set /p x=
    set /p y=
) < settings.cdb

IF DEFINED x (
    IF DEFINED y (
        ECHO true
        GoTo :EOF
    )
)
ECHO false
GoTo :EOF

In Java, I have the following code to call the batch file via command line:

ProcessBuilder probuilder = new ProcessBuilder(command);
Process pr = probuilder.start();

BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));

String line;
while ((line = input.readLine()) != null)
{
    lines.add(line);
}

X and Y are some input parameters from a configuration file, which may, or may not, contain any data.

When x or y are not defined everything works as suppose, outputs false.

The problem comes when the variables are both defined.
When the batch file gets called via command line I get the resulting output: true. <br/>Which is the intend output.

When I call the same batch file via Java Process I get the following output:false. <br/>Which is not what I want.

Removing the @echo off I get the following output from running the batch file from command line:

IF DEFINED x (IF DEFINED y (
ECHO true
 GoTo :EOF
) )
true

But when I run it from Java Process:

IF DEFINED x (IF DEFINED y (
ECHO true  
 GoTo :EOF 
) ) 
ECHO false 
false
GoTo :EOF 

It is not even outputting the echo true.

I've tried with EXIT /b 0 instead of GoTo :EOF but with the same result.

So what am I missing here? Why the program, when called from Java, keeps going even though it has a GoTo :EOF?<br/>
Why the different outputs? Is it a Java thing? Is it a batch thing?

UPDATE:

After all the file from where variable were being loaded is relative to the command line location instead of the bat location.

Well, you said it: "It is not even outputting the echo true". When you add debug lines, it.. helps to think for a second about what it means. 'x' is not defined, or 'y' is not defined (or most likely both are not defined).

You can manage the environment of the spawned process, use ProcessBuilder, and before launching (with e.g. start()), first set up the environment; for example with pb.environment.put("x", "hello");.

Why are you running batch scripts from java, though? They were bad technology back in the 80s, and there are a ton of alternatives available at this point. If you explain what you're trying to accomplish by farming work out to a batch file, perhaps an enterprising SO reader can make some useful suggestions.