This ../ is added for the each folder you navigate in the Publish New Page dialog. The workaround to this issue is, before creating the new page, navigate to the folder you want to publish the page. So while Publishing, you can directly publish without nagivating to the folder in the Publish New Page dialog. The code also is not corrupted.
Hope this workaround help you.
Thanks for your advice; this does work and stops the include line from corrupting.
Why Contribute should try to add ../ outside of the quotes I don't know; if it was adding this to the path of the include file it would perhaps be an understandable bug, but not the way it's doing now!
Is there absolutely no other work around or fix for this problem at this time? We have several users using Contribute for our site, users who are already used to this not being an issue in CS4. We'll be fixing a lot of templates even if we do manage to retrain everyone on this, just because people will forget.
Thanks for the workaround. We have the same problem and your solution works. Hopefully, this will be fixed in a future release.