It isn't exactly something I'd consider an issue, but somehow I've managed to cause the cheats to be permanently persistent.
In other words, even after restarting the game, all cheat effects are still persistent. Additionally, the trainer doesn't function any further on that particular save.
On a fresh save, the trainer works as normal, and the cheats are not persistent when properly deactivated. I'm not exactly sure what I did to cause this issue, but if I run into it again, I'll be sure to leave a report as to how I duplicated the result.
Again, it isn't an issue. I'll just consider that one save file the "Cheat Save".