You bring up a good point Stabby.
Like you said, the Transmutation [Polymorph] rules state that "You can only be affected by one polymorph spell at a time. If a new polymorph spell is cast on you (or you activate a polymorph effect, such as wild shape), you can decide whether or not to allow it to affect you, taking the place of the old spell."
..and Enlarge Person is merely a Transmutation spell, not a Polymorph spell, so it wouldn't come into conflict with the Polymorph rules.
But then again, there is the "Multiple magical effects that increase size do not stack" rule and both Wild Shape and Enlarge Person are magical effects. I don't think my GM would honestly think of "setting" and "increasing" your size as different effects. I mean, they still, relatively speaking, increase the size of your character, by the definition of the word.