Hey! Sorry my reply is so slow >.< I'm working on some stuff for Spooktober VN Jam again this year, so I haven't really been checking here since I've been super busy with that.
I don't suppose you managed to get it to work in the end?
Unfortunately, there probably isn't any advice I can offer, which sucks :( I know that what you said it a common-ish problem with games made in Tyranobuilder because back when I used that engine, I was searching for answers myself and came across several support threads on their Steam pages from other devs asking the same thing. As far as I'm aware, it was never fixed >.< The devs of the engine just said to people, yeah, that happens sometimes and we don't really know why, but usually it fixes itself... It was that sort of attitude towards fixing bugs in the engine that made me decide to stop using it (among other reasons.)
So yeah, I have no idea why it does that for some people and not for others :( Are you on windows or mac? Cos I think it probably happens to more people on mac, though I've seen it can still happen to windows users. All I know is that you're not even supposed to see the nodewebkit bit. The game is just meant to launch when you click the exe >.< If the nodewebkit thing is coming up, something has somehow gone very wrong.
I can't even do any investigating because I don't use the engine anymore >.< I made SR and Impostor with it, then got fed up with how buggy it was and switched to Nani x Unity. So I'm sorry I can't be of more help :( It really sucks to be powerless to do anything when someone actually wants to check out one of my games >.<