in this case please contact the support team http://support.plarium.com/ensparta/Tickets/Submit/Step1/52
There has been a few topics on this kind of issue since last server update...
http://plarium.com/forum/en/sparta-war-of-empires/bug-reports/29570_message-lag
http://plarium.com/forum/en/sparta-war-of-empires/bug-reports/29988_galleys-sign-don-t-turn-off
http://plarium.com/forum/en/sparta-war-of-empires/bug-reports/29884_message-outstanding
Yes plarium I know it has been an outstanding bug, but last server update has made it much worse, maybe something to do with new screensaver. At the moment I have 3 unread messages symbol(when there actually is none unread). Then I have 3 galley reports, when all have been seen, plus I have a missing galley report as one trade only gave delivered report not the received res report. The new screensaver freezes all timers until page refreshed - galleys, raids, returning units etc. If the screensaver comes in view, then your city is attacked after that, you will not see report or even know about it until you have refreshed page!
Temporarily corrected for a day.
My reports and messages were cleared, but now 4 ghost reports again today. Timers locked up also when away from screen. Don't notice screensaver anymore.
I hardly care if you fix it or not now, this game will always be full of bugs and lag. The important things top of your list are money spinning new features which are currently about as well received as a floating turd in a swimming pool.