Why would some flashing lights on a model show working fine in the storm tool, but not work ingame?
Well, it could be any number of things; a miss-spelled node, an error in the sprite files, even miss matched files (e.x.; the sod has new lights on it, but the sprite file doesn't have any mention of the new nodes). It can be narrowed down with a bit more info though, have you added any new ships with custom lights, or installed a mod that edited any of the sprites (Lights, Nebulas, weapons, ect.)?
Yes, added a new ship that uses the stock flashing lights (attached to the correct 'lights' part of the hp structure). They are showin fine when exported to sod format in the storm tool, but dont show ingame. They also have the correct name (i.e: s_yellowstrobe_1, _2 etc.....)
Wouldnt that make them not show in the storm tool?
hm sounds strange. what i know is, that, if some events happens ingame, blinkers stop blinking. For example have a look at the federation yards with their blinkers, as soon as you repair a ship and the yard animates, the lights stop blinking.