I would say that PW would ignore the effects of the map. assuming that the map rules are game effects.
I honestly have a hard time discerning some of the rules that are not game effects.

Taken from the awesome map review article review from Saturnflight:

Shadowlands

A character cannot target a character, object, or square more than 6 squares away.

From Pulse Wave:

Draw lines of fire to all other characters within the area of effect, including at least one opposing character; these lines of fire ignore all game effects except for walls, blocking and elevated terrain.

I would think map special rules would be considered Game Effects. That said, the Shadowland Map rule would come into effect when Pulse Wave attempts to target a character in the Area of Effect. Since the determination of Pulse Wave's AoE ignores all game effects that are not walls, blocking, or elevated terrain, and the special map rule isn't any of those three, it should be ignored.

Also, the effect of Pulse Wave ignoring "effects possessed or used" is done after AoE is determined. Determing AoE is not limited to effects that are Possessed or Used.

TL;DR, Pulse Wave should ignore the Shadowlands special terrain rule when determining the Area of Effect.

I'd agree. The map effect would be ignored by the line of fire. If there were a map effect that affected something other than the line of fire, for example if a map reduced damage done to characters, that would not be ignored since it is not an effect used by a character.

As for rules vs game effects, we are working on a better way to differentiate between types of effects and clarify the entire system. I'm not going to talk time frame but it is something that's happening.

I agree with you, only you are mistaking, the AoE do not ignore anything, the LoF is that ignore game effects.

the PW's AoE is determined by the halve of you range after all replace and modify of your range

so if you have a character with 13+ of range you can still target character with 6+ square of you with PW