It's funny that you should post this - I literally just finished tuning up a friend's StumpJumper. Learning that I can still tune a bike to ride like that put a smile on my face.
Sounds like a bad bottom bracket to me. What kind of bike is this? Bottom brackets rarely match the level of components you see on the rest of the bike. If you ride a lot, I'd recommend investing in a really
nice replacement. High-end Shimano, like LX or XT. Of course these days the bottom bracket spindles are splined. If you bike is older with the squared spindles, you might have a little difficulty finding the right bottom bracket - especially in the right length.
I know the bike only has 2,000 miles on it, but all it takes is one good submersion to compromise the seals or lots of dust to grind them away.