30 fps and below on Minecraft and 60 fps stable on Battlefield 3, why?

Try reinstalling Java. All I can think of. By the way, don' be surprised if when you fix it you still don't get over about 60fps. A lot of people underestimate minecraft because of it's simple looking graphics and assume they should be getting 100000000000fps non the game when in reality there's actually a lot more going on in there than you think.

Minecraft isn't a hard game to run, but because of the settings, you might get lower FPS than predicted. Try turning down your distance rendering. If it's on far, your computer will try to render practically a HUGE portion of the minecraft map. On top of that, while you move your computer has to remember everything that you've done, destroyed blocks, buildings and so on. At the same time it has to also render more of the map while you move.