Let's see if I can describe this in a meaningful way!
I've noticed this for a few releases and am finally getting around to posting about it. When I restart The Brain, the app "forgets" the past window size settings.
I frequently detach files to my desktop and then drag them into my brain. To make this easy, I shrink the window a bit so The Brain doesn't take up the whole screen and I can see part of the desktop. In the past, the sizing was "remembered". However, now when I resize the window, the size only remains while the app is open. If I close and restart The Brain, the size reverts to what is essentially a maximized window.
In other words, clicking the Maximize button doesn't do much to change the window size. Upon each restart of The Brain, I need to again drag the window edges to resize to my liking.