I only had that happen once, one thing to try is using the AFNI layout files. Once you retrieve the files using Mission Control, use AFNI to: Define Datamode --> Misc --> Save Layout. Then you can play with the starting places of each window/controller. You can use a layout as the default, or launch AFNI with -layout <some_file>.
With our multi-monitor setups, we then alias AFNI in the shell by putting something like the following in your .bash_profile:
alias afni1='afni -layout /Users/Shared/AFNI/monitor1.layout'
alias afni2='afni -layout /Users/Shared/AFNI/monitor2.layout'
