Window and palette locations are not remembered on dual-monitor Mac

Mac OS 10.11.4 (El Capitan)

Mac Pro (early 2008) 8GB RAM 2x 2.8Ghz

This two-monitor Mac was upgraded from Lion to El Capitan yesterday. Everything’s great except it is not remembering window locations between start-ups. So if I drag my Safari window to the 2nd monitor, then quit and restart the Mac…Safari opens again on the 1st monitor. This is true for every application…it seems that window locations are ‘remembered’. I have to re-arrange my windows during every session. It’s not just Safari…it’s many applications (Calendar, Pages, Numbers, Safari, Mail) but not all (Calculator, App Store, and others remember their window positions).

The Adobe CS6 application palettes (tool palettes in Photoshop, Illustrator, InDesign) jump to my first monitor any time I switch to a different application and then come back. For example…my ‘pages’ palette will be placed on the second monitor, then I switch to Illustrator and come back to InDesign (no quitting, logging out, etc.…just an app switch) and all my pallets will jump over to my first monitor.

What’s going on? How can I stop this behaviour? It’s getting quite annoying.