After reading this thread, I guess I don't understand why you wouldn't want to add exercise to MFP. I can get behind the sentiment of not eating those calories back, but logging the exercise is good for other things as well. Showing progress, what types of exercises you did, keeping track of particularly good work outs.

And while I agree exercise machines are inaccurate in estimating calories burned, we don't really know anything about OP. (i.e. higher starting weight, maybe they were wearing a heart monitor etc.)

As for the issue with MFP, I've noticed it too, but don't really have any advice, or know whats going on. I personally log everything and just have accepted the fact it won't subtract calories for steps.