We read up a little bit from what information was available, only to find that anyone who had the Another Ver. had discovered absolutely no differences. You can see that in sales posts like this. I even asked Cave via their twitter account where Masa King used to reply to practically everybody, but the topic of the PCB was never responded to. Funny enough, this was a while after the Mushi Futari 360 port came out. So from our memories of the Japanese version of the PCB and the recent 360 port, we compared things to the international version.
Because we didn't have the Japanese PCB at the time, we made small comparisons with the 360 port. We weren't finding much difference at all, except for two things: 1) You couldn't "stream" gems from the first boss's head in between his life brackets. 2) Bosses in original mode had slightly less health - my hypothesis was approximately 20%. Using science (control of variables is playing on Original with Reco, ONLY using laser, no bombs, which is why I die like an idiot on the 360 sometimes), I posted these on my YouTube channel on Cave-STG, and EOJ put it up as news on the front page.
Xbox360 Stage 1 Boss vs International Version Stage 1 Boss
Xbox360 Stage 2 Boss vs International Version Stage 2 Boss
Xbox360 Stage 4 Boss vs International Version Stage 4 Boss
For a while, that was basically all we had for information. The internet (okay, maybe like, 2 people) clamored for more. Well, now I have a Japanese MFBL PCB. So Alex brought over his Another Version yesterday, and the two of us, with the help of shmups members Jeneki and Aquas (because Kiel was still working and Poodude's in Portugal), did some science!
For all pictures and video, the International "Another" version is on the left in the New Astro City, and the Japanese version is on the right in the Egret 2.
Pictures:
Boot-up screen


Legal Screen


Title Screen - Notice how the International version has cool colors for the little forest spirit things, and the Japanese has warm colors. The International version also has the "Another Ver." underneath the logo.

Now the comparison between the Japanese PCB and International PCB. Again, Original mode, Reco, only using laser, no bombs.
Japanese Version Stage 1 Boss vs International Version Stage 1 Boss
Japanese Version Stage 2 Boss vs International Version Stage 2 Boss
For a little more science, Alex and Aquas had a Maniac Mode face-off on the Stage 1 Boss.
International vs. Japanese Stage 1 Boss Maniac
What do you notice? Here's what we noticed.
1) Health is exactly the same on Maniac mode for the boss(es).
2) Bullet patterns are slightly different. Maybe they are programmed differently? For example look at the pink Pac-Man Ghost shaped bullets at 0:10. On the International version, there are about 4 bullets per "wave" but in the Japanese version there are 6-8, making it a much smaller gap between bullets.
Other things we've noticed playing these two boards:
1) God mode seems to be identical in patterns and in health. We haven't done much video of this because one run of God mode is not very similar to the next, even for the same player. Sometimes things go very very wrong. Sorry, I'm not Clover-TAC.
2) Changing the difficulty level in the test menu seems to do absolutely nothing at all. So it's not like upping the difficulty on the International version really changes anything.
3) Backgrounds are all the same, enemy sprites and patterns are the same. One thing I had thought when I saw the title screen was that maybe the little sparkle-trails behind enemies would appear differently because the difference of colors on the title screen, but they are the exact same. So it doesn't appear that any art assets were changed within the game between the two versions.
Aquas or Jeneki may pop in here and give their thoughts as well.
I still have both boards in the cabs right now since Alex was kind enough to let me borrow them. If you have any questions of things I should check out, please let me know and I'll do what I can! I'll probably enlist the help of Aquas for some of it... The guy's a beast...