afni.nimh.nih.gov

Glad you got this worked out. The solution is strange, and I don't have El Capitan, so this will be a little hard to test. How are your multiple monitors set up? Are they equivalent resolution? Do you still have the same problem if you switch left and right monitors? There has been a long, on-going thread on similar issues over various Mac OS versions including a workaround using the Mission Control preferences.

https://xquartz.macosforge.org/trac/ticket/796