I hate to necro my own post, but it's three years later and Avernum 3 has the same damn bug. What the hell, Jeff? I still haven't played Avernum 2 because I've been waiting for this to be fixed, and it's still broken in Avernum 3. Seriously, this is the last Spiderweb game I'm buying until you fix this. It's 2018; monitors have been widescreen for a very long time.
Have you contacted Jeff - email@example.com -about this at all? He is usually very good at fixing problems. If not, try GOG support, maybe they can help.
I think we are having the same issue. Between this and the lack of cursor lock and having multiple monitors, it makes the gme a bit frustrating. I asked about this on the steam forums https://steamcommunity.com/app/691830/discussions/0/1699415798757005797
His response was this.
Spiderweb [developer] Feb 1 @ 2:29am
The game makes the window a tiny bit smaller that the whole window. If I make a game window and don't do that, I get weird mouse interference with the start menu (Windows) and the dock/menu (Mac). If you want the game window to fill the screen, just play full screen. You can Alt-Tab to switch applications.
Feel free to post over there and maybe he will finally look at the issue and make it work. I thought I was the only person that had an issue with this.. issue.