I followed the instructions exactly, left the boxes for song title and album unchecked (I generally knew them already) yet it changed them for hundreds of songs and I have no idea which ones. I now find incorrectly tagged songs on a daily basis that I knew for a fact were correct before I used MPFreaker.

It'd be easy to write this story off as "He probably didn't follow directions and checked the boxes for song title and album", but do so at your own risk. At least test it on a few songs before you run your entire library and watch the dialog box extremely carefully. The only pattern I've noticed is that it seems to switch song titles of the same artist.