Abbyy Finereader 11 has training mode, where we can teach program how to interpret special characters.
http://www.youtube.com/watch?v=LAJm3J36tLQ
I don't know though, if there is possibility to force Abbyy to automatically show formulas as images or at least whole line (if there is some mathematical expresssion inside), instead of doing it manually page by page.
I still use Abbyy or Acrobat for detailed or quick ocr-ing of k2pdfopt files, even though there is ocr capability within app now.