I downloaded the retail version of tghe trainer and started it as administrator. The game crashed when I got a hostage in the church killed and went to retry that mission it crashed then.
This could be like with Arkham Asylum, where if you failed the Scarecrow sections with infinite health on, the game would crash.
Here's what I did after getting stuck after the Ras Al Ghul gliding trials (like everyone else, after you do the glide/dive trials and you end up in the room, no assassins are there to greet you up the stairs, and you can't go past the invisible wall which appears to be SecuROM reacting to the trainer's presence/usage):
Start a new game. DO NOT start with the trainer active at all. Don't even open it.
After you first get the Batsuit on top of the Ace Chemicals building, alt+tab out, and run the trainer. Press F1 when you're back in the game's pause screen.
Then, just use the "99 Upgrade Points" cheat, NOTHING ELSE.
Immediately alt+tab out, close the trainer out completely. Back in the game, just glide to the courthouse where you save Catwoman and trigger the first auto-save checkpoint once you get inside. I recommend using the 2nd floor door.
Once you're in the courthouse and the game has saved, just ALT-F4 completely out of the game. Now restart the game, and go ahead and just max out your skills/upgrades with your points. If you do this, SecuROM doesn't detect the usage, and you'll have pretty much everything you need maxed out for the most part(armor, health, skills, gadgets, etc).
Now, you won't have infinite health, etc., but with everything upgraded from the start, Batman/Catwoman are both already pretty OP. I had no problems getting through most of the game on Hard with only using the trainer at the above one point in the game. Most importantly, it allowed me to get through the Ras Al Ghul fight and I finished the game. Am now enjoying it in the New Game+ mode.
Also, the game did NOT crash ONCE on my playthrough where I only used the upgrade cheat. On my previous playthrough where I used Infinite Health and let the trainer run the entire time, along with the upgrade cheat, I got crashes 20-30 min. at a time and never got past the invisible wall in the Chamber of the Demon. Hope this helps!
Quoting myself here...
No knock on the AWESOME job the CH guys/Caliber has done, but I just would not trust using anything but my above method with this game, at least until a patch is released to fix the DX11 and Ras Al Ghul/invisible wall glitch...
SecuROM is just so wonky that a trainer (any trainer) can cause it to trigger a gamebreaking glitch or corrupt your save. It's happened to probably everyone who actually leaves a trainer (any trainer) running for any period of time (again, Ras Al Ghul invisible wall glitch, Wonder Tower glitch, missing NPCs/triggers/cutscenes, corrupt and missing saves, etc).
It's not GFWL/Xlive because it's already been mentioned that CH trainers have Xlive protection built in, so it has to be SecuROM and to be honest, that's anyone's guess as to what kind of crap it's capable of when it prematurely detects a trainer and thinks the game's integrity has been compromised..
Just to add more info, I ran multiple trainers/CE tables on my save game. Just before I got to the Ras trials, I exited out of the game and reloaded with no trainers active. I was able to get pass the invisible wall glitch with no issues.
I do agree though, its either SecuROM or remember that Arkham Asylum had a little copy protection scheme built into it too (remember the cape glide not working on illegal copies?) I wonder if the invisible wall is the cousin to that and is a little sensitive to things running in memory (hence why legal copies are seeing it too).