Ok, now I understand, you are not seeing the runway lights straight-on, but from an angle, and yes, they are supposed to look like that because, being entirely custom (not made with the SDK) they don't use the lights effects and they don't rotate in view with the user, to save performance.
What mislead me was the sentence "lights at each end of the runway are standing vertically instead of laying flat.", these are runway side lights, they are not supposed to be flat in any case. And they are directional, you are supposed to see them less from an angle.
The ones that are flat, are only the centerline (if there's one) and the green on the centerline of the taxiways, but the light component will always be vertical in any case, because it's the only way to see them from a reasonable distance, without looking squashed on ground when you get close.