Paul,
Some food for thought here, but we'd need more info to really offer more help.
Questions:
1. Does this happen in neutral (not just with clutch in)?
2. Does the bike start and run OK at first?
3. Is there a noticeable lack of power?
4. What's the plug look like?
Since it's a new bike, I'm guessing it might be fuel or compression related, nothing disastrous like bad rings, etc.
One thing might be compression. Improper compression on a new KLR could result from poor valve clearance. This should have been checked around the first 500mi/805km or so (every 6000 mi/9660 km after that.) Was that done? Did the dealer or local shop do it? Did you get a printout with the measurements? I would never trust a dealership to do the first 500mi
check/adjustment correctly, if at all. It seems a likely place to skimp. If it was checked and you have the numbers, was
it close to begin with? The valve clearances will tighten over time. Maybe sufficient miles have been accumulated to bring the valves out of adjustment.
How long has this been happening? After a recent fill up? Could be bad gas, drain and refill from another station if you
suspect.
What oil weight are you running? Incorrect oil viscosity could cause problems, clutch slippage too. (remember the clutch is
a wet clutch and shares oil with the engine.)
If it's brand new, and you haven't done the valve check at ~500 mi, I'd suspect that first. You can do this yourself if
you're at all handy. There's plenty of help online and even a video you can purchase to show you how. Best place for the
video, service manuals, and valve-shims is:
http://www.arrowheadmotorsports.com
In case you don't know about the Yahoo KLR group, go here:
http://groups.yahoo.com/group/DSN_klr650/
Best place to get technical help. If it happens to a KLR, someone on that list will know what to do.
Good luck.