In all previous versions, basecamp would remember that I want on my secondary monitor and would start up there. Now 3.1.1 always insists on starting on my primary monitor, so every time I open it I have to move get out of full screen mode, move it to the other monitor, then switch back into full screen mode. This is a pain.
I understand the issue you have explained. This is indeed something we will investigate for a future release.
I too used to launch some apps (Outlook) on the secondary monitor always, as a personal preference. To better understand your particular use-case, can you tell me why you want to launch BaseCamp in the secondary monitor always?
Because I'm frequently trying to plan trips and looking in my browser for motels (prices, availability, etc.). My browser is always open on my primary screen, so I like basecamp in the secondary screen.