how long have you had the juniper??
it may not be a disease.... it may be a variegated chinese juniper just doing what it does, turning yellow.
id never seen one until about six months ago when I was at my local bonsai nursery and noticed a juniper with yellow patches, I asked Leong what was going on and he explained it is a Juniperus Chinensis auro-varigata. below is a pick of the tree after it has been sitting in the corner of his nursery for 15 years, and another after he gave it a style
D'angelo I think Paul is right, you have possibly the worlds first variegated kishu shimpaku Sorry couldnt resist im in one of those moods