Signals do not flash, they work in initialise, but after Call ("endUpdate") you can´t Call ( "beginUpdate", again so signales they are later in track will not flash.
This game has British, German, Swiss, Austrian, American, Chinese, Japanese & Turkish signals Without further information nobody can help you
Didn't think about it, but it's a general problem when the game loads, either directly go from -1 to flash or when the game is running it works ,it won't work when it comes from other signals, in initialise of startup game, so be careful if the train stay 1-3 signals away.
Still no information on the route you are having a problem with. Tell us and we might be able to help On some routes the signals do flash for junctions On some German routes a flashing Green or yellow indicates a change of speed Have you read the manual for the route you are have in the problems with?