Hmm, using the trainer with ALT at the end (www.cheathappens.com/trn.asp?trnID=34864), I don't activate it until I'm actually in a campaign. Once the campaign is up I hit F1 and start turning on whatever options. After that it's simply a matter of turning off the trainer with / (it has to say DEACTIVATED) at the end of the turn OR when playing a manual battle. Some agent actions can also cause CTDs when options are on, so it's best to leave agents and armies close to battle until you've done everything else, turn off the trainer and then do assassinations or battles.
For anyone who is experiencing crashing when ending a turn either in the midst of playing or when you load a save then end your turn, the below worked for me...
I am on the latest version of both steam and Last Samurai. I was able to play the game fine with the trainer so long as I did not close the game and load my save. After I did that there was nothing, no combination of trainer options (or no trainer at all) that would prevent the game from crashing after I ended the turn.
The following link kills some temp files, I have not experienced any adverse effects from following the instructions.
Let me know if it works for anyone else, this was driving me crazy. I could play for hours using the trainer but if I stopped for the day and loaded my save the next day it would always crash. I tried many fixes, this was the only one that worked.
The trainer is so simple to use all you need to do is turn all options off before you end your turn, also it would be wise to turn it off before you head into battle or before you pick retainers as the game might crash otherwise.
The trainer will also not necessarily work with the the torrent version of Shogun 2, so don't expect to get any support here for it.
I don't know if anyone experiencing this as well but when you tried to destroy your own ships, it crashes. Not always but quite a few times and sometimes turning off the trainer didn't fix this problem.