I've noticed that when I use auto-hide, The Brain version 7 takes a performance hit everytime I mouse over the blue circle and it appears. Seems to be linked to the number of icons in the view--- the greater number of icons, the faster the degradation of all performance overall. Simply revealing the brain 20 times when I have 30 or more icons in the current view is enought to have it slow down to take several seconds on ANY action, from displaying the thought icons (instead of the default circle or blank square), to responding to keyboard input. Adding a new thought can take up to a minute. Continuing on without closing down means version 7 taking longer and longer to "reveal" (redraw its icons and other items) after being revealed from auto-hide.
After noticing this issue particularly strongly with extended views, I began testing with auto-hide and normal views, and even there its performance can be seen to degrade with each "reveal". Extended view just exaberates the issues in my usage because my extended views tend to have many more thoughts in the plex at a time than normal usage.