Could you please specify what exactly is the problem when you leave the trainer running and just activate it again?
The primary problems seem to be based around options NumPad7 and NumPad8, Unlimited Resources and Unlimited Resources On Transfer respectively. I first noticed an issue with these two optionns (I did check to see if the trainer had noticed the game and was activated).
After that I discovered that all options to do with Unlimited Ship Health, Super Ship Speed and Super Speed, F1, F2 and F3 respectively also failed to perform correctly.
Please note that I am now over 80 hours in game and would have noticed before now if these functions working.
Any way I can be of more assistance, please let me know.
Paul