When I try to use iedit in a buffer with flymake errors, flymake's overlay overrules iedit's match highlighting because it has a higher priority. I made the following change to fix it:
--- iedit.el (revision 1784)
+++ iedit.el (working copy)
@@ -76,6 +76,11 @@
+(defcustom iedit-overlay-priority 200
+ "The priority of the overlay used to indicated matches."
+ :type 'integer
+ :group 'iedit)
(defcustom iedit-current-word-default 't
"If no-nil, use current word by default for the occurrence."
@@ -271,6 +276,7 @@
(overlay-put occurrence 'insert-in-front-hooks '(iedit-occurrence-update))
(overlay-put occurrence 'insert-behind-hooks '(iedit-occurrence-update))
(overlay-put occurrence 'modification-hooks '(iedit-occurrence-update))
+ (overlay-put occurrence 'priority iedit-overlay-priority)
(defun iedit-make-unmatched-lines-overlay (begin end)
200 is a higher priority than highlight-current-line (60) and flymake (100) use, but lower than show-paren (1000) and auto-complete (9999) do.
(Excuse the svn diff format.)
I have integrated the change to the master branch.