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I use the borders on my site for the links at the top of every page. The only problem is that it doesn't work for most of the pages (curiously, it does work on an entire directory of them). I know FP includes the borders at save, and when I open them up on my computer in Firefox they look and work fine. When I publish it to the server it breaks.
Strangely enough, I tried opening up the site with FTP in Explorer and dragging and dropping the good files from my comp onto the server. They still broke.
Does ANYONE have any idea why FP would do this? They work fine locally...
It would be extremely difficult to say without seeing some of the code.
However, from your description it might be worth your while to consider replacing your shared borders with Include Pages. If as you say there are only links in these borders, then FP can track and set relative links just as well in an Include Page.
I thought that whatever was on the HD was what was published, but nooo, FP wanted to redo the borders with the server-side border files. I ftped the good border files and commanded FP to not touch them, and things are looking good now.