Commit bd1b57f92a33485c90db1efc407c8b7c7450993a (Thu Sep 2 11:35:43 2010 +0000) 
did something like this in org-html.el:

               ((str (org-export-html-format-href thefile)))
-             (if (and type (not (string= "file" type))
-                      (org-string-match-p "^//" str))
+             (if (and type (not (string= "file" type)))
                  (concat type ":" str)


This broke the exporting of [[file:a.org]] links, which now appear as 
[[http:a.html]]. Try C-c C-e H on any .org with such links, even in emacs -Q.

The problem is, I think, that „type“ is actually "http", not "file" as the code 
tries.

-- Daniel

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