My adviser wants to use bad statistics. Help! I am going to submit a paper in a couple of weeks. The results are good, but my adviser wants me to report the results in a particular way that makes them artificially look better. I asked a statistics professor about this method and he emphatically said it was dishonest and the wrong way to report results. I argued this with my professor and he would have none of it. I told them the results are good anyway, why report it in this inflated way, and he insists that this is simply a difference in opinions on the definition of this metric. He says he has published many papers with this metric and other (major) people in the field have used this metric too. But when I google around I can't find a single source that jibes with his definition.

Clearly I am unable to convince my adviser. I am uneasy being the first author on a paper with dishonest reporting (especially since honest reporting would not impact the worthiness of the article). Some of the other coauthors are uneasy too, but we're just grad students. I'm tempted to change the numbers to the right ones right before I submit the paper. What do you recommend I do?
Do not "change the numbers to the right ones right before I submit the paper" - this would be submitting without your co-authors approval.

If you are sure that "your" statistics are the correct ones - which sounds likely in this case - get back to your advisor with your other co-authors and the stats prof, try to convince him once more. Support your opinion with papers and/or textbooks.

Depending on how wrong your advisor's suggestion is, insist on not using it, or let it over to reviewers.