Yep, that's basically what the problem is in a nutshell.
The trainer works perfectly just as intended, except that for those who do not use any of the troop options, just activating the trainer locks out the normal, vanilla "untrained" troop reinforcement.
So basically to recreate this - load up EU4, activate the trainer, go into any battle, lose a few men, go back into friendly territory and wait for them to replenish - with the trainer activated they won't.
Edit: Just so that there's no misunderstanding, this isn't a showstopper by any stretch of imagination (at least not for me) and you've provided ample options to work around it; it's just an annoying niggle for those of us who prefer to keep the military aspect realistic, for a lack of a better word.
[Edited by mackintosh, 1/17/2014 11:21:23 AM]
you do realize you can replenish instantly ANY troop by pressing:
F5 Key: Refill Unit
maybe I am still confused..
best,
Cal