Changing output freqency in bonkenc portable?

I can't seem to find an option for it.
Mainly because I downloaded a FLAC album, and it's a 24 bit sampling rate and 96000 hz!
It would not work on my mp3 player after I encoded it using bonkenc portable to ogg q3.
It would play, but really slow and crappy.

So I was wondering if there was an option somewhere.
I figured it out on audacity portable, but you can only do 1 file at a time, so that's very inconvenient for me.