Some instruments have odd resonances, some strings sound louder than others at certain positions and some notes are louder than others. If you find a note that always sticks out, find the frequency of that note and create a little notch filter using an eq and pull it down, make sure the notch is quite narrow. Don't just throw a compressor on it and turn it up, that will just ruin your dynamics.
FREQUENCIES: What are the frequencies of bass notes? - FAQ courtesy of GollihurMusic.com