Problems With Indmar Engine

I have a 325 hp Indmar MPI engine in my boat. The engine starts fine and runs well under all conditions except one. Strangely enough, the boat chuggs and backfires for about half a minute after it sets for more than an hour after being run at normal operating temperature. You have to constantly pump the throttle the whole time it is chugging along to keep it running because it will not idle and just dies otherwise. Once you baby it through this little episode it runs fine again. You can shut off the boat for 10, 20, 30 or 45 minutes and it will start right back up with no problem. It starts up cold just fine too. I seems to only happen when it is still warm but has been sitting for more than an hour.

Has anyone else had this problem or know what might be causing it? It is sort of like vapor lock but I was under the impression that EFIs don't get vapor lock.