Well,
here is what we discovered: We don't know if that was because our VB6 application was executed on the command line,but it was actually using the MS-DOS environment default charset, which in our case was the windows-1252.
So, all we had to do was to change our Java code to something like this:
InputStreamReader inputReader = new InputStreamReader(input, "windows-1252");
and it just worked fine!
Maybe it's even not because of the MS-DOS environment, but because we are getting this data from a Microsoft Access database. Personally, I think that this is the most probably solution for our problem.