It seems like anything that gets in the engine bay ie. MUD, water, anitfreeze always ends up on my hood as well with the splatter effect. I had a similar problem and found it to be a leak in the radiator getting blown up (possibly by the fan) onto the inside of the hood. Not sure if it is related to your problem jus a thought.
1998 Chilired TJ 4.0, 8.8, HP30, 4.10's, 4" Superlift, OME shocks, 15x8 MT classic locks/33x12.5 PJ's, Warn flares, Flex-a-lite elec fan, k&n intake, Cobra Cb, KC's, AtoZ rockers, ARB front bumper, LoD rear tire carrier