today i was making sitewide changes, previewing them one by one. everything was alright at building time. but when i upload everything, all the links went haywire. they point to non-existent pages within directories. for instance, i have a directory search/overview.html. and a directory first_steps/ask.html. just now when i previewed on the server, the link that points to search/overview is pointing to first_steps/search/overview.html and the other one points to first_steps/applying/ask.html and every link are pointing to directories within directories that don't exist!!
I'm comfused with your explanations but could putting a / infront of the URL's help? Making the link start from the root.
it's ok now, i manually change every link in every page, lost a few visitors during the time . it's the one in my sig if you're curious.