I attempted to flag this question on Christianity.SE...
...as "off topic". Although the initial flag dialog loads correctly, every time I selected the "it doesn't belong here, or is a duplicate" option, the next pane would fail to load:
Request URL:http://christianity.stackexchange.com/flags/questions/18136/close/popup?_=1375739403107 Request Method:GET Status Code:404 Not Found
The account had 46 reputation. I tested this on other sites, but found that it only occurred on Christianity.SE. This was my only account that has the for the flagging privilege but not enough for the comment privilege.
I have now earned the commenting privilege on Christianity and am no longer able to reproduce this error, confirming its cause.