When I change my desktop background on my primary display, it also changes on my secondary, but it still shows my secondary display's selection in the SysPrefs. I have to change the size for it to come back up.
anyhoo, also I have a problem on a login when my menubar items appear, they also flash in the lower right corner of my 2nd monitor. The 2nd monitor is positioned to the left.
I ran 2 and even 3 monitors for a while. got too hard on my eyes and I went down to the one largest. there are minor issues now and then with stuff like that. its not perfect technology. unless it puts a damper on the over all use of the system then just try and overlook it. dual display problems usually always work themselves out anyway as the one has with you. the other one will also i'm sure.