This applies to the stable-3_3_0 version: Once the ROR plugin template is loaded in the contributor modal, the placeholder text "Search ror.org" is displayed in other taggit fields as well:

The issue is caused by the jquery selector used in affiliation.tpl ('.tagit-new > input'), which is to unspecific.
A possible solution is in the template file to replace each occurence of
$(tagitInput).attr("placeholder", rorPlaceHolder);
with
$('input[id^="affiliation-"]').parent().children().find("input").attr("placeholder", rorPlaceHolder);
Yours
Felix