I heard the question on NPR's Car Talk this morning. It's so interesting! I have to know the answer!
A quick disclaimer though: I'm not sure if America or Japan made the switch to 31 caliber. The radio made it sound like it was Japan, but the website (http://m.cartalk.com/the-puzzler) makes it sound like it was America. Vague pronouns suck.
The Japanese tried to switch from .30 to .31 (from the Type 38 Rifle to The Arisaka Type 99). My understanding was that it was a range issue -- the .31 caliber rounds are more accurate at a distance.
The switch was far from complete, though; the Type 38 remained standard equipment until the end of the war. As a general rule, Japan's industrial faculties weren't up to the total revamp of armaments most outside observers (and some internal ones) believed was necessary. So no "switch" was really made; it was planned, but realistically a long period of peace would have been necessary to bring everything -- including service rifles -- up to date.
Cartalk now broadcasts old content, they are no longer recent. I found the relevant answer on another site, see below.
RAY: And the Puzzler question very simply is: Why did they do that? Of all the calibers out there, why did they make a 31-caliber rifle? Well, one part of it, I think, is pretty obvious. And that is, if they had to vacate a position and their ammunition were captured, it would be unusable to the Americans. What hap? Too big! It doesn't fit in the rifle!
TOM: That's right. It would stick.
RAY: But the other part of it isn't so obvious. If the reverse happened--that is, if we...if the Japanese captured our ammunition, the smaller-caliber bullet would fit in their rifles, and they would be able to use our bullets to fire on us.