This has "fixed" my issue (turning off the option of "separate spaces" in my multi monitor setup), but having "separate spaces" and its associated functionality of the menu bar and the dock appearing on whichever display I happen to be working on is something that I have grown to LOVE in the new OS's. This is a significant step back for me to have to disable this.
I work with three Apple Cinema displays, currently with a mix of graphics cards in my Mac pro - ATI and NVidia, I'm hoping I will solve the problem by replacing the ATI one with another NVidia one, and perhaps using the NVidia drivers (which don't seem to be yet updated though for the recent point one update of El Capitan, or weren't last night when I looked).though
(Although other posters in this forum seem to suggest it is a problem with two of the exact same Nvidia cards in a machine. Ugh.)
I'm heading to the shop later today to buy another NVidia card, I'll report my success, or lack of it.