Well, I know (taking Banished for example) it can take up to 27 seconds for that trainer to start. Although I had the wrong version, the trainer detected "GAME ON," and when I activated, just as you said, it froze, and took a good 30 seconds to start. Since it was the wrong version, it crashed right after with CheatEngine.exe not responding as you had described.
I fixed this by verification of both game version and trainer being correct (Except in some cases), or waiting some time until after activating each and every cheat (Take Rome Total War 2 Trainer for example. It takes 3-10 seconds per cheat to activate at times, and if you do too much, it crashes)
Give it some time prior to activating each cheat, if that doesn't work at that moment, personally, I'm unsure.