One thing I've noticed is that heteronyms can give TA some problems. Depending on where in the sentence and/or if it is capitalized will result in different pronunciations. Could there be some way that TA would flag these words in a different color text so you could check and make adjustments so it would read right?
Wikipedia has a list of examples at http://en.wikipedia.org/wiki/Heteronym_(linguistics)
that show's what I mean. The big ones I have noticed so far are nice/Nice, read, minute, and live. I bet others can elaborate on this from their experiences.
Just an idea.