In minibuf-eldef-setup-minibuffer there is this form

    (add-hook 'post-command-hook #'minibuf-eldef-update-minibuffer nil t)

I think this is not correct.  The APPEND parameter of add-hook should be
t so all changes made to the minibuffer content by previous functions in
post-command-hook are taken into account by
minibuf-eldef-update-minibuffer.

Here is a patch for the trunk.