Okay, one more stupid question: You said you were testing against several bandits and whatnot. Were you trying to use the Shout on a bandit while he/she still had allies attacking you? If so, then yes, they will resume attacking by design. A successful 'Submit Shout' sets their aggression to 0, however, they still belong to a hostile faction, and if they see any of their faction allies attacking you, they will re-agro on you. It isn't until after you talk to them that they get added to an additional faction which has the side effect of making them simply run from hostilies from that point on.
Unless, of course, you were trying this against a lone bandit or whatever that had no nearby, visible allies. Then I don't honestly know. I spent the entirety of last night taking the most recent version and adding new functionality to it, and after using it dozens, if not hundreds of times, as I started/stopped/started/stopped/etc Skyrim over and over to test it, I never experienced them refusing to talk to me after they submitted and dropped agro.
And with ~500 downloads of the most recent version, if I truly borked something up in the mod, I would expect others to be in here telling me to pull my head out of my ass because I suck at modding and should DIAF.
So, with nothing else that comes to mind, did you try the old disable mod/save/reload/save, re-enable mod, reload the last save game. Or trying to go back to an older save?
I will say that in my work last night on the new functionality, I lost ~1.5 hours thinking the new content wasn't working and I made a mistake somewhere in the implimentation. Then I realized that it was all because of the stupid nature of Skyrim that doesn't allow you to do a proper clean save by simply disabling a mod then saving. I loaded a slightly earlier save game and discovered it was actually working perfectly. And by that point, it was pushing midnight and had to call it quits for the night.
So try that, and if still nothing, dunno. I expect to be updating with the new functionality tonight, so maybe that will play better for you.