Not sure what do you mean by wbs extension as I've never seen a single file saved with that extension when playing civilization.
I have all of my maps saved same way - *.CivBeyondSwordWBSave extension. It's just those maps I copied and pasted into new files using MapView, are working differently (starting in 4000 BC, instead of 6000 BC).
I tell you what - there are some good examples of that you can download from here:
http://forums.civfanatics.com/downloads.php?do=file&id=17662
forums.civfanatics.com/downloads.php?do=file&id=17664
forums.civfanatics.com/downloads.php?do=file&id=17665
forums.civfanatics.com/downloads.php?do=file&id=17666
forums.civfanatics.com/downloads.php?do=file&id=17667
If you could check one of them and tell what's possible to fix it I'd be delighted.
Sorry i don't have the time atm to do any of that.
The suggestion i made was like that:
When you open a *.CivBeyondSwordWBSave (*.WorldBuilderSave for Vanilla, that's why i said *.wbs) you can easily tell the actual map design apart from other things like player setup, map conditions and whatnot. The actual map are the thousands of lines that contain all that begintile and endtile things.
When you just copy and replace that part into a working map, you can be pretty sure it will work. (I hope). But you need to adjust some things, like the mapsize in the part you took over from an existing map.
But take care, player starting positions, signs etc.