I have the same issue as well. Steam version here. I tried turning off and on the option during the gameplay and that seem don't have affect on it.
I have the same issue. Other players is reporting the same issue as we have in other Halo forums. It is highly unlikely that it is the trainer. Also I have the same issue with checkpoint in Halo 1.
Once you died, the checkpoint will function as normal. I assumed that it will happen in every chapter but I found that it only happen every game session. What I do is to try to die first within the start of the mission before going on my way so I can force the checkpoint to function. I am not sure if it is a "feature" (intended by design of the game) or it just a bug that majority of the players haven't encountered since they are usually to die within 5 min.
I noticed that it only will not work on covenant weapons that are using percentage (Energy) as an ammo. Plasma Pistol, Plasma Rifles, and Energy Sword are those weapons that use percentage and the trainer does not work on them. On the other hand Needler, Brute Shot, Fuel Rod Cannon and Carbine use actual ammo and the trainer work fine with it. I have not tested on Beam Rifle and Sentinel Beam yet but I will not be surprised if Sentinel Beam couldn't work. I have the same issue on Halo 1.
I tried both options (Num 8 and 9) and one of those option only. It didn't matter, it will not work on them. And I tried the one with EAC disabled and replaced the mcclauncher file.
I'm sorry, English is not my native language. I am having difficulty understanding your last sentence with the double negation. Are you saying you made it work? It is working fine on your end? If that is the case, then that option is not working on my end. If you need my save file, I will be gladly to share it to you for you to analyze it.
I tried the updated trainer that is released today too.
I can confirm that this is indeed bug after latest update, since many others that play the game have gotten same problems in missions, that game progress is not checkpointed anymore, some even had to start missions all over from the start.
So this has nothing to do with trainer, rather with broken game update.