@Arliss –
My theorizing about the same change we made last year was wrong… that code is still in.
The problem has to do with the relative positions of the monitors on your desktop, and the fact that one monitor is in Portrait, and is taller than the others (in pixels). We’ll figure out how to make this better, but not for today’s release. It’s not the simple change I hoped it might be.
The good news is that we can reproduce your issue here, although it involves turning a laptop on it’s side because we have no monitors that will do that for us! 
On the DoxCycle front, Colan will respond. For the long term we will solve that with Option Profiles, but we likely will not have time to incorporate that feature in DoxCycle in the next month or two.
~ Cameron