Not sure if it will for others (if they haven't already tried it) but ah move to the Cockpit/Ship Control page and that usually sorts it out (sometimes click the General Events button if going to the Cockpit doesn't work)
I encounter this quite often, but for me it is only happening with sublight, ascend/descend and cross terrain travel, not once has it happened with hyperspace travel and ground travel within a city (that I'm aware of).
I think I recall reading somewhere that it has to do with the difference between the local timer in your browser and the timer running on the server. The server "checks" the server time only every five minutes or so with regards to travel, so that it doesn't claim too much resources from other game functions, or something like that. Emphasis on "I think..."