> SET password=a^b
> ECHO %password%

> run the_name the_pass^word

> run the_name "the_pass^word"

java...config.user_name=the_name config.password="the_pass^word"

java MyClass username=%~1 password=%~2

> run mr_clean puke^^^^boy

> run mr_clean "puke^^boy"

java MyClass username=mr_clean password=puke^boy

e.g.:  my_batch.cmd the_pass^^^^word

@echo off
setlocal Enabledelayedexpansion

set variabl=-^^"^^-
set variabl
echo delayed !variabl!
echo percent %variabl%

--- Output ---
variabl=-^"^^-
delayed -^"^^-
percent -"^-