What makes you think that c:\windows\system32 is not your current directory? The user.dir
property is explicitly to be "User's current working directory".
To put it another way, unless you start Java from the command line, c:\windows\system32 probably is your CWD. That is, if you are double-clicking to start your program, the CWD is unlikely to be the directory that you are double clicking from.
Edit: It appears that this is only true for old windows and/or Java versions.