I actually had this issue too, and I am not sure why it happens. The trainer does fine but if the game crashes while you a few options activated then those options will not work if you do not also close and reopen the trainer. I think the reason for this is because of how abrupt the crash can be. Now in my case it is the game crashing, and not reopening the trainer. While it looks like the game has reset, if you never reopened the trainer then the options you had previously are still activated in terms of the game but not the trainer. Thus, causing the error. It really only happens when the game crashes and I don't reopen the trainer so I have no idea why it takes 3 tries for you.
My experience: I start the trainer first and then the game. I get to the main menu and activate the trainer. Then I go more into the game and start playing while activating any option I want (super damage in this case). The game crashes or freezes all of the sudden, and then I just close and reopen the game. Since it looks like the trainer reset I reactivate the trainer and start toggling options. Next thing I know I am trying to toggle Super Damage but it gives me the same error you are getting for whatever reason. I close and reopen the trainer, activate it and still the same error message. That is when I closed both the game and the trainer so they both reset. Once I got back into the game and activated the trainer everything worked fine after that. (it's happened more than once for me)
To put it briefly: I go in-game, turn on trainer, activate super damage. Game crashes, reopen game, activate trainer, error on super damage, close and reopen trainer, activate trainer, super damage still error, close both game and trainer, reopen trainer, reopen game, activate trainer, super damage works.
I have no idea why this is, my best guess is the game's code being finicky.