Hiya - best for your peace of mind to get it listened to by a dealer - Lee mentioned crank failure just now, there was a motor with a failed countershaft bearing a while ago which caused a bit of hoohah, and of course the early 800 series motors had too much piston clearance which made them rattle and chug like diesels, but an '09 bike shouldn't really have this particular problem.
The Rotax unit is on the whole very well put together, but like most things is subject to the odd unexpected failure - after all, nothing's perfect is it? (just don't ask a 1200 owner cos despite everything he'll claim it actually is!)
You could try to identify the root of the noise by having a poke around with a long screwdriver. Put the handle into your ear and touch the pointy end on various parts of the engine while it's running - it acts like a doctor's stethoscope like this - you'll hear all sorts of things going on, it's quite interesting actually!
Best of luck
Greg