I'd suggest to get a *.wbs (or whatever it's called for your extension) that works well and manually replace all the map data from the file created by mapview and leave all other elements unchanged (just apply the changes manually that you know are save to change).
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.