No idea...please post  if you find a solution. I thought I saw something on
codeplex that would convert URLs in pages. Might be worth a look.

Have you tried an stsadm  backup and restore. I've used this method
successfully and haven't had problems with the wiki  urls. I don't
think it would change hard coded urls this way, though.

Backup/restore has worked fine to get me from farm 1 to farm 2 within
its origianl location. I am now try to move the wiki  from one site
collection to another. To be more specific, I am converting a
subsite with one part be a wiki to a new site  collection. With the
help of stsadm.blogspot.com and the gl-convertsubsitetositecollection
command everying is going great except for the wiki.

I have even tried a 3rd part tool that is suppose to be excellent for
content migration and it is having the same problem.

metalogix and/or Echo? If one of those, they should offer a way to do this, or
at least support your issue.

just checking...

I tried Metalogix demo and converts the [[page]] as well but did not
look at Echo. My Wiki was pretty small so I just fixed things
manually but it would be intereting to know why this occurs.

Do you have a single wiki  library? I moved the Wiki library in .net, created an
empty wiki lib and read the pages, parsed them with the correct URL and stored
them in the new one. I had some glitches with pictures (forgot to move their
URL) but resolved it by running through the pages and replacing the url with a
simple command line.