Happened me too, the trainer messed up the dragon souls for me and I can't learn any more new shouts, even though I've more than enough souls to use. Even tried using console commands to reset souls to zero, then killed a couple dragons and got new souls without the trainer - doesn't matter, still can't learn new shouts. Something with the trainer messed it up. Ah well :/
Like I said its not an offical patch and sinces its a mod. I doubt it will have its own trainer version. As they then would have to keep up two sets then. As there is people that do not use that mod.
All trainers are tested on vanilla games. Yes mods will or could possibly mess up the trainer, If the mods change the game *.exe file in anyway to what the trainer is looking for then your trainer may not work. So be warned. Trainers are not likely to be made for mod versions.