Do you hear the auto decomp kick in at low revs when the bike is running?
I am having the same behaviour on my 640 and my cam was replaced only 6000kms ago (as a result of the infamous cam roller bearing failure) and the auto-decomp has stopped working.
So I wouldn't discount the auto comp not working just for low mileage.
But, I would (and will) look at the other things Gunner suggested.
2005 KTM 640A