The issue occurs frequently - and I mean really
frequently, i.e. every few minutes - when switching through cities with the senate window open, but it can also occur in other situations - and it occurs with and without user scripts active, and it occurs in IE, FF and Chrome, and it does not depend on the duration of the session. (As we all know long sessions can cause quite a number of updating or synchronization issues but this one can happen also only minutes after a new log-in.)
Of course I remember the "call of the ocean" issue - and that´s why I have been trying to find any such regularities during the last ten days, but it´s not that easy this time. The only regularity I could detect was this one: The issue occurs more often while construction or recruiting orders are going on in the respective city. That´s why I encounter it much more frequently in zz5 than in zz1 or 2.
Firebug shows an "uncaught exception" supporting this observation:
When switching through cities with the senate window open and construction orders going on, I have the impression that the updating of the city name in the UI seems to lag a bit behind - until I come to a point where only the city name in the senate window is changing to the one of the next city while the city name in the UI gets stuck - and from that point onward you cannot click anything before pressing F5 to escape the freezing of the game situation.
When staying logged in during the night, you sometimes also will see this situation in the construction queue in the morning:
In fact this construction queue is full (real construction orders, not "ghost" orders) and they should be displayed as 7/7, not as 1/7.
However, as I already told you - there are no real regularities I could find, only situations where the issue tends to occur more often, and a correlation with running construction orders seems most likely.