Ok so this is a rather strange bug. Previously I thought it was simply a performance issue (see MC-2850) but upon further investigation this seems not to be the case. After starting to ride the minecart as soon as you leave (what I believe is a single chunk) where you started there is no longer a rail riding sound and it starts to lag. You can get off the cart and walk around and it continues to lag. When you back to the chunk you started the sound is still playing and it stops lagging. Even exiting to the menu does not stop the rail riding sound. For the rest of the session even if you exit to menu and go back you will lag outside of that original chunk until you restart the game.

Update:

The bug is no longer occurring. No idea why.

Update 2:

Not sure if anyone will still check this but the bug happened again while I was playing and watching a podcast on Ustream at the same time. This leads me to believe it's conflicting java processes that is causing this.