I once had a mysterious leak in my SXIPro. My jet ski mechanic suggested I take the battery out before putting it in the water to visually check the shaft seal. With the battery out it didn't leak until I pushed the rear of the ski down so water entered the tray, then I could see water dribbling in.
Turned out the plastic bracket which holds the E Box in place was missing a small screw and bolt at the bottom. The screw head (countersunk philips head) is covered by the padding at the front of the tray so you normally can't see it. It must have vibrated loose. The screw and nut went missing but the countersunk washer was still there.
Put a dab of silicone underneath the washer, replaced screw and nut, leak fixed.