You might also try its more modern cousin, ProcessBuilder:

Java Runtime.getRuntime().exec() alternatives

Perhaps you should use waitFor() to obtain the result code. This means that the dump of the standard output must be done in another thread:

String path;
String[] params = new String [3];

                    params[0] = "D:\\prog.exe";
        params[1] = picA+".jpg";
        params[2] = picB+".jpg";

        try {
            final Process p = Runtime.getRuntime().exec(params);
            Thread thread = new Thread() {
                public void run() {
                    String line;
                    BufferedReader input =
                       new BufferedReader
                         (new InputStreamReader(p.getInputStream()));

                     while ((line = input.readLine()) != null)
                         System.out.println(line);


                     input.close();
               } catch (IOException e) {System.out.println(" procccess not read"+e);}
            };
            thread.start();
            int result = p.waitFor();
            thread.join();
            if (result != 0) {
                System.out.println("Process failed with status: " + result);
            }

I think you are confusing about the exe arguments. Try this one:

private String appDomain = Paths.get("").toAbsolutePath().normalize().toString();
private String exepath = appDomain + "\\src\\bin\\exeResources\\MyExe.exe";
private String exeargs = "silent-load";

try {
        Runtime r = Runtime.getRuntime();
        r.exec(exepath + " " + exeargs);
    } catch (IOException e) {

        e.printStackTrace();
    }

You're on the right track. The two constructors accept arguments, or you can specify them post-construction with ProcessBuilder#command(java.util.List) and ProcessBuilder#command(String...).

Here is a link to another question with a very detailed answer on how to do this correctly in an async way with threads. This is the only way to not block your main thread and hang your GUI.

private class ProcessResultReader extends Thread
{
    final InputStream is;
    final String type;
    final StringBuilder sb;

    ProcessResultReader(@Nonnull final InputStream is, @Nonnull String type)
    {
        this.is = is;
        this.type = type;
        this.sb = new StringBuilder();
    }

    public void run()
    {
        try
        {
            final InputStreamReader isr = new InputStreamReader(is);
            final BufferedReader br = new BufferedReader(isr);
            String line = null;
            while ((line = br.readLine()) != null)
            {
                this.sb.append(line).append("\n");
            }
        }
        catch (final IOException ioe)
        {
            System.err.println(ioe.getMessage());
            throw new RuntimeException(ioe);
        }
    }

    @Override
    public String toString()
    {
        return this.sb.toString();
    }
}

then you use the above class like so

try
{
    final Process p = Runtime.getRuntime().exec(String.format("cmd /c %s", query));
    final ProcessResultReader stderr = new ProcessResultReader(p.getErrorStream(), "STDERR");
    final ProcessResultReader stdout = new ProcessResultReader(p.getInputStream(), "STDOUT");
    stderr.start();
    stdout.start();
    final int exitValue = p.waitFor();
    if (exitValue == 0)
    {
        System.out.print(stdout.toString());
    }
    else
    {
        System.err.print(stderr.toString());
    }
}
catch (final IOException e)
{
    throw new RuntimeException(e);
}
catch (final InterruptedException e)
{
    throw new RuntimeException(e);
}