If you develop in PHP on Emacs, then you’ve probably got a hook setup to run flymake-mode on PHP files. And if so, then you’ve also probably noticed that this doesn’t work with nXhtml, which will often return an error like “mumamo can’t find the file” (or some such), causing flymake-mode to disable itself.
The culprit is likely to be a bind like this:
(add-hook 'php-mode-hook (lambda () (flymake-mode t)))
which says, “turn on flymake-mode when php-mode is started”. (Sacha Chua has a post that recommends using this from couple of years back.) The problem, as far as I can tell, is that nXhtml tries to process the fleetingly available _flymake file rather than the original PHP script whenever it toggles into php-mode.
A better hook to use is the find-file-hook, like this:
(add-hook 'find-file-hook 'flymake-mode)
With this, Flymake will properly validate PHP chunks in nXhtml mode, as well as any other files that Flymake is smart enough to process.