I had this happen to me as well, but not since I finished upgrading the botnet abilities. Maybe manually upgrading them breaks its 'unlimited' power?
I just restarted game and it hasn't happened since.
Either run the trainer before the game. Click your exe. Splash screen appears. Then click or alt/tab to Steam and answer the hidden prompt to allow command lines, after that the splash screen will disappear and game will load fine and trainer will work. Alternatively, start the game on your own with the correct parameter, then alt tab and start the trainer, hit cancel when it asks for exe location and then use trainer normally.