I can't find a way to reproduce it properly, but it happens too often, as i have switched to the 11362 SVN build (was using Beta). Usually this happens when i get first message after i login to Spark. Any subsequent messages doesnt make chat window to flash in the taskbar either. But if i try to login with another messenger on the same computer and then send a message to my JID on Spark, then it starts flashing. Also if i go to Preferences and uncheck, check again Flashes and save, this seems to fix this issue for a moment.
This ticket needs further investigation to find proper way to reproduce it.