Shifting Trouble
 

Hi everybody, this is my first bike so please don't get too mad at what probably sounds like a dumb question.
A new 06 rockhopper I bought shifted flawlessly the first time I got on it. After the trial run I took it out on the trails for about three hours or so after which I started getting loud clunking noises shifting up no matter how little load it was under and sounds down right nasty under any pressure.
The shifting has gotten progressively worse over the last couple weeks and now it seems like the deraileur isn't aligning to the cogs at either extreme. From the center and small ring on the front shifting into the last couple largest cogs on the back results in missed gears, gears not engaging properly, going up hills in these lowest gears sometimes results in the chain popping off one cog to the next.
On flat trails when on the largest ring in the front and the smallest two or three rings on the back if I want to shift up or down I now have to shift two positions to get the chain to change position at all. Even coasting and turning the pedals very slowly under no load at all doesn't help this, if I only shift down one from the highest gear I get nothing, I have to shift another, and then shift up on two get to the second highest gear.
Now it hasn't been four weeks since I bought the bike and the LBS said to bring it back after five or six weeks of heavy riding but I think I'll be taking it in tomorrow.
What I wanted to ask was: is this what normally happens as cables stretch and parts break in? Or is something wrong with either the shifter, the deraileur, or the cables? I have had it through the mud a couple times, springtime in New England is a pretty muddy time, but I cleaned off the cables and don't see any obstructions or anything.
I guess I just basically don't want to walk into the bike shop with it totally blind as to what to expect done, so opinions (constructive opinions) would be helpful.

Sounds fairly normal, probably just cable stretch and some adjusting needed. Go ahead and take it back to the LBS for it's first tune-up if it needs it. And here's a site that probably explains adjustments better than I would:
http://www.parktool.com/repair/readhowto.asp?id=64

If the bike is new, the shop should look at it free. Most offer a free check up/adjustment in a 30 day time period.

Yeah it sounds like the typical cable stretch. You can turn the cable adjusting barrel 1 or 2 clicks counterclockwise and it should take care of it. As far as components you'll find they last a very long time and may even outlast a frame. My 17 year old mountain bike has all the original components with the exception of the front derailleur(which was my fault for cycling with long pants).

Thanks for the quick responses, I think I'll take it back in tomorrow. It hasn't been thirty days yet but I have been riding a lot and do weigh a lot more than average. I think the wheels need some truing as well.
One other thing that may not be normal though is pedalling is not all that smooth, if you pick up the back of the bike and turn the pedal by hand it feels a little "gravelly" like the bearings in the crankset are grinding a little. Might they just need to be packed with more grease?
I weigh about three hundred pounds, not fat just very big, am a avid backpacker with very strong legs. I have no bike skills yet so hope I haven't destroyed anything.

"One other thing that may not be normal though is pedalling is not all that smooth, if you pick up the back of the bike and turn the pedal by hand it feels a little "gravelly" like the bearings in the crankset are grinding a little. Might they just need to be packed with more grease?"
It may be that with the DER properly adjusted, that may disappear. Could be just the misalignment of the chain/cogs, which the adjustment will fix.
Have the shop check it out though.
Good chance the wheels need truing.