iMac 5k collects second (vertical) monitor windows to main monitor after sleep, restart, etc.

I love everything about my 5K, but this is driving me nuts. I'm using my previous monitor (Dell 24") as a second monitor in the vertical position. When I wake from sleep or after restart, many and sometimes all of the 2nd monitor windows are collected to the main iMac display. Occasionally, for certain apps, their second display windows will be moved over even after simply selecting another app and then returning. The main offenders that I work with are Excel, Messages, Safari and especially Photoshop Lightroom. In the case of Lightroom, the fullscreen vertical window is resized to fit the iMac display, so I have to move it back AND resize it in order to continue working. I had hoped the upgrade to El Capitan might help, but no luck.

Does anyone have any idea what could be causing or how to correct this behavior?