Even though I mentioned above at 400 hours I would think riser problems would have appeared long ago, I did not discount your input. I've heard from a couple different sources that riser height can be an issue, especially on single engine boats where the engine sits lower in the hull. Below is the only picture I have of the exhaust with the engine in the boat. As you can see, I cannot add the 6" riser extension that is the only one I can find available for the 496. Not enough room overhead. I've got the shop that pulled the engine looking at the y-pipe flappers and the tailpipe flappers for missing parts. If they report back everything is intact, then I would suspect additional riser height might prevent this from happening again. I just wish I had the room to add the extensions.

I would like too see some pics of your manifold / riser height. IMO once you posted that you had side exhaust I would not rule out what I posted for reverting water. Also IMO I think your riser height is too low -

I did not read very many of the posts up here so I might have missed something on top of, but again to add I would like to see manifold / riser height and in relation to waterline height.

Side exhaust can be a real problem with reverting water especially with a boat in rough water conditions that has full gas tanks, along with many people on board and any added equipment ie: batteries, coolers, ice, tools, camping gear, tool boxes and so on.

It is the standard aluminum manifold/stainless riser setup that would have came on any '03 496 Mag. With the boat sitting in the water, the side exit exhaust tips sit above the water line. Even piling a bunch of beer drinkers/hell raisers on the swim platform will not dip the tailpipes into the water. The boat reverted water either when I pulled onto the trailer to go get gas or backing off the trailer returning from getting gas 30 minutes later. Water was dead calm and I was the only person on board. No crazy gear load inside boat. I keep minimal gear/clutter on the boat at all times. Here is a side view of boat. Water line is right about in the middle of the bumped out style line just up from the chine.

My guess would be backing it down the ramp could force feed water up the pipes, especially if it is a steep ramp.

Very weird exhaust , if I'm seeing it correctly. Almost looks like for the exhaust to go to the side exits, is has to turn back .

Maybe a non issue, I don't know, but when I haven't seen something so 'un normal' I just have to state that. LOL.

SB side thru exhaust is extremely popular for the past 15 years with Sea Rays, Crownlines, Cobalts, Bryants and so on with family rec boats. The problem is when a wave hits the side of the boat - and that side of the boat dips down and then hikes back up to the other side can revert water if the manifold riser height is not tall enough. Common problem with this type of install with riser height too low and wave slapping. Also very stern heavy boats the same applies

Common Sea Ray with the common side thru hull exhaust

https://www.youtube.com/watch?v=N98YvYs0-B0

and another hot rod

https://www.youtube.com/watch?v=wEfTrqXaNhk

Correct. The exhaust comes back forward slightly to exit out the side. I've seen more extreme cases of this on other boat brands with side exit. Has work fine for 11 seasons and 400 + hours. That's why I'm hoping we fine broken/missing flappers somewhere. Otherwise it will be a head scratcher. Wish I had access to the boat but it is in storage at the shop that pulled the engine and I'm still not medically cleared to drive after a surgery I had in January Shop owner was supposed to look at Y-pipe and side exits and report back but you know how that goes.

I'm sorry, I am not saying that this has led to water ingestion issues, I'm just saying, excuse the french, this is the most retarded exhaust change of direction I've ever seen. That's all. Just talking out loud.

I don't disagree! It should have been routed out the back. But the way the transom is inset makes it a bit challenging so they went the path of least resistance and stuck it out the sides. Like BUP said, there are tons of different manufactures that run this setup and some come back forward way more dramatically than mine.

Shop finally called back. Both flappers missing in y-pipe. Which is what I figured based on when the boat reverted water. I just didn't see the source being the side exits. At least now I know the source/cause.