> I am not sure whether Emacs can work around this or not.

I don't see an easy workaround.

> Perhaps one approach would be to not use the glib file-polling code.

That sounds like it may be the best way forward, at least in the short run.  If 
you configure --with-file-notification=inotify does the problem go away for you? 
  That is, does the attached patch work for you?