i don't know if this is what is effecting you, but something that has happened more frequently now for me, is that after an end turn, the unit hightlighted as selected, centered on, is not the one that is actually selected, so all the options are wrong,if i have any, if i move one unit, its a guess as to which one actually moves. etc. sometime it shows a unit selected but is actually selecting a city.. ugh. trying to select the unit doesn't do anything, since it sorta is already selected. you have to click on something/someone else, and come back, if this is infact whats happening to you.
so like raven-sb said, make really sure your sovereign is selected.