GROUP BY Returning Different Totals
I followed @ypercube's suggestion and just rewrote both queries - turns out there wasn't a relationship in the database that was needed to tie two tables together, and when there were multiple relationships on a set of columns MySQL did what @JNK said and was non-deterministic and grouped inconsistently.

If you run into something like this, check your table relationships, especially if there are multiple possibilities with what you're joining on and you only need to be joining on one.

Thanks for the help everyone.