I've been fiddling with JSOW's for the last couple of days (looks like I've picked a good time to study that subject lol) and I ran into the same issue. Been reading and watching everything on the subject trying to figure out why JSOW's in PP mode miss targets by at least half a mile. Also, wanna add that bombs never open, they just fly past targets and drive straight into the ground.
The latest test I've done:
TOO + waypoint designate (waypoints created in the editor, on the targets, ground level) = hit.
TOO + TPOD = 2 hit, 2 overshot and hit the ground (maybe more testing needed, maybe the same bug).
PP + manual coordinates (same targets created in the editor) = overshot by at least half a mile, bombs never open, drive into the ground.
F-18's coordinates format set to match F10's.
Tried both magnetic and true heading. True is the right one, but bombs still overshoot.
Also, before that tried creating waypoints manually (in precise mode) and using them in TOO + designate. That also resulted in a miss.