I also enjoy creating maps in WorldBuilder, though not Earth-based ones. I have noticed that natural wonders I place sometimes migrate. Usually I get some warning as I work on the maps in multiple WB sessions, so I have a chance to notice, for example, 'hey, that's not where I left Lake Retba.' Sometimes I can 'pin' a wonder in place by surrounding it with terrain it can't appear on, leaving it with only the tile where I placed it to remain. That worked with Lake Retba on my most recent map, but the Pantanal wound up jumping a river onto tiles that had resources on them (which I had thought would work to pen it in, but no, apparently only the underlying terrain will prevent wonder shifts) so it was extra wonderful that game, heh.
I think your options are either using the terrain-fencing method, or seeing where the wonder 'wants' to go and adjusting the rest of your map to compensate. If there's some coding trick that would help, that's well above my pay grade.