Ok.....here's what is happening. First of all you need to understand that when you look at a texture in Photoshop/Texview and even the preview screen in the PBOManager window of WRPEdit your texture looks like this:
1 2
3 4
When you add it into your list of surfaces, and the way it will be placed on the island (and appear in game) is like this:
3 4
1 2
That's the way it is....I found the easiest way to think of it is that "North" and "South" get reversed, "East" and "West" don't.
Now onto texture rotation. If you have an EW runway and you want to make a NS version, the temptation is to just rotate it 90 degrees. Don't do it! Here's why:
Lets say this is your texture, with 1,2,3,4 being the "background" and the line being the runway.
1 2
----
3 4
When you rotate it, you rotate
everything:
2 | 4
1 | 3
So your background texture may not fit with other textures around it, even though the runway will.
What you have to do is keep you runways and your background textures seperate until both components are in the correct positions
then merge them into one. You are going to have to learn to use the selection tools, plenty of copying and pasting, merging and flattening layers etc to get around this problem. It's way more tedious I know, but the results are worth it.
There you go!
(Should I just make a tute?....it's almost one already)