Notwithstanding that the fuel gauges say that the tanks are 1/4 full, have you dipped the tanks to make certain? And are the valves set so that fuel coming from any given tank to an engine goes back to the same tank? Otherwise you may be returning fuel from both engines to one tank. Which may in fact be full.
If you are certain beyond doubt that each engine is drawing from its respective tank and returning to that same tank, and that fuel is not mixing from one side to the other, then perhaps the vent to the tank on the side that's spitting up is clogged and air isn't able to exit the tank when you are fueling.
If you determine the boat is spitting up, you can try feeding the boat slowly and then holding the boat to your chest after she's done feeding, patting her on the hardtop. Some soothing music may help. You can also think about changing the formula- maybe a different brand of diesel fuel might help.
If you think your boat is choking or vomiting, then try holding the boat upside down and firmly patting her on the back.
If all those measure fail, you may have a colicky boat. In that case, she may benefit from a ride in the car. Just bundle her up in the back seat- make sure to use a certified car seat- and take her for a ride. About twenty minutes or so should do it. Then, carefully, without waking her, put her back in her slip. Don't forget to hook up the shore power cord.