Drop the leading /
and change your includes to
include("../footer.php");
the leading / means from the root of the file system.
You are digging below the root and there just ain't nothing there.
Another thing to beware of when dealing with problems between windows and linux is that on windows ../footer.php is the same as ../Footer.php which is not the case on linux (case sensitive vs case insensitive file systems).
UPDATE
The final solution was to for the relative path for the include into a absolute one by prefixing it with __DIR__
as in ...
include(__DIR__."/../footer.php");