Hi there,
I'm on a Mac running 10.11.1 and have three monitors. When I open the AFNI GUI, the windows move quickly to my leftmost monitor and disappear off the edge. They're still "open" and running because they show up when I gather open windows in Mission Control. The issue is that they won't stay up in active mode. When I just use one monitor--the one on my iMac--the GUI windows stay open and everything is cool.
I know that mine is probably an early adoption of El Capitan but wanted to put this on your debugging radar...
Paul