Sorry if this is telling you how to suck eggs, and I'm assuming that you're using the TPOD as opposed to manually entering co-ordinates; but I've had JDAM accuracy issues when I haven't been high enough, I think if you lase them whilst you are fairly low or at an oblique angle it screws with the co-ordinates. I get good results from 12-20k ft either aiming at the base of the target i.e. the ground underneath the target or sometimes nearly directly over, basically as close to perpendicular as I can get away with.
