you don't have to update the firmware when you reformat or do a disc cleanup.
as for the click, is it within the first second and just barely there? i get that too with the disc cleanup/reformat. i've hard of other people having it too. i don't know if anyone else figured out how to fix it or what, but i usually just edit it out in post.
for me the format/cleanup helps keep the little blips and digi noise type clicks and junk out of the recording. however, i don't think everyone has the click/blip/diginoise problem, just some. which is kind of weird.