This has happened to me too. My SH3 install was fresh and i followed the order of installing the mod and patches etc, I even removed all traces of the old installation prior to the current install of SH3. However it appears that the boxes seem to only appear when the attack angle is at it's best position, then and only then is the best time to shoot.
I don't think the boxes need to be colour coded, looking at them (the boxes) you can tell which box represents what section of the ship.
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