@soulflame - read most of your posts, didn't have time to read each of them in-depth. I ran similiar tests, and at first it looked like enemy fleets and armies (enemies to my trading partners that is) that were in potentially threatening positions might be the cause of the blinkers.
However, I found one internal city, no overseas trade, all sea trade was with my own cities, yet it had the blinks. Dispersed my nearby fleets and troops, just to make sure A) no possible enemy/rebel nearby and B) it wasn't the "fog of war" along sea routes that caused blinking. Nope, clear as could be. Since the blinking was between CityA and CityB, i checked CityB - no blinks. No sense, how could CityA's sea route be threatened, but CityB's route is fine? Then, someone over at .com said it looked like cities with Shipwrights and above always get the blinks. So, I checked out every single city and sure enough, that was the case. Shipwright and above - always blinking, Ports are always fine. Total trade income in these cases was always the full (blinked) amount every turn.
But, sometimes, blinking is correct - if you just attacked a faction you trade with (or they attacked you), that turn you'll see blinking but in this case, it's for real
edit: forgot to mention, when i was running my tests I was only at war with the Gauls who had no navy, so there wasn't a single boat in the Med that was a direct threat to me, except for the rare rebel ship I've seen once.
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