If you haven't already you need to assign the JDAM/JSOW bomb a GPS target by clicking on tgt (I think it was) on the MFD and then click on the buttons coresponding with up and down to choose from the GPS marked targets such as DMPI-1, DMPI-2 etc. With JSOW you need to stay high up to launch it to have any success hitting any targets (at least that is wat I do, but i don't use the JSOW that much).