I happened to be flagging two comments as obsolete (on this answer, comments referring to a completed edit).
I flagged the first, then clicked the second flag button, and upon trying to flag (I am not sure if I made a reason selection) the You may only submit a comment vote every 5 seconds message appeared.
When I attempted to flag again I got a warning like Please select a reason for flagging. After waiting or dismissing the message and trying to flag the comment again, the "You may only submit a comment vote every 5 seconds" warning appeared again, and so on, in a circular fashion; I was not able to get the flag dialog to appear to select a reason.
I was able to successfully flag upon refreshing the page (but did not think of that at first in my confusion).