I found CRPro's interface not really user friendly (for example too many clicks needed to choose the correct reference) and had it correct references to the wrong files (completely other filename...), even when the correct references were choosen.  Last time I tried it, it  was just sitting there doing nothing at all on the scan, maybe my runtime's too big now.
One good thing about it is that it writes a log file so you can find those errors - it's poorly formated thought, but if you use an editor that highlights all occurences of a certain filename, checking what it did isn't too bad.