Huh, okay now it appears to be a random event. Playing last night and I warped out of a system and the warp flare was suddenly green again. Was thinking "Alright they fixed it". Entering the next system however the warp in flash was red, but the beam down was green. After finishing the mission the beam up was red and the warp out flare was red again.
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Valuable feedback guys. I suspect this will be sorted, it's probably something related to why KDF Toon creation is unavailable at the minute The faction itself will be overgoing some overhauls before launch I guess.
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I too agree the effects should be based on the ship. If you are in a Rom ship then Rom effects, KDF ship then KDF effects, so on and so forth. It is stupid to have the allies technology override what is going on with my Rom character flying a Rom ship.