Ok, I May have some sort of clue for you.
I too was running into the issue with the trainer suddenly "not working."
It IS working, but not when tabbed in to the game, I have to alt tab out and click on the CH window to activate the trainer options.
Now, this started for me last week. This could have been a Win 10 update thing like others have said, BUT another notable change for my system, was I finally received my HTC vive. So perhaps the HTC vive installed some drivers that altered the way windows deals with background programs? Perhaps the other posters can specify if they too just recently received a Vive headset. I also bought "virtual desktop" off of steam.
I hope this information helps you narrow down the culprit.
EDIT: Should clarify that im not actually using the headset or virtual desktop while running into this issue.
[Edited by Mocking_crow, 5/1/2016 4:44:47 PM]
I am sure users of that device will appreciate any feedback you have about using it. We do not have that device so we can only rely on users to report back how to use our trainers best with them
best,
Cal