Seems in my reshuffle of the difficulties I accidentally doubled up on the easy/hard changes (since I realized that where I did have them would potentially not have changes viewable in preparations), and forgot to remove the extras in the first chapter, so the units were getting double the buffs they should. It's fixed for the release coming in a few minutes.
Also, you can save on any turn so long as none of your units have moved yet, just by opening the menu like you would to change options or check the objectives. I'll make a note of that in the quick SRPG Studio primer I have at the beginning and in the tutorials.