As for why I am renewing that one now, the reason for that is I tried getting a certificate for a NEW server and it failed. So after a bunch of thrashing I decided to take a step back and try renewing a certificate that recently worked to make sure it wasn't me (well, okay, it might STILL be me). I did run into the problem you mentioned with too many verification failures on the new server I tried which is another reason I wanted to try an already-working configuration.
As an aside when I was debugging this problem over the past few days I did see a few "Internal errors" reported from boulder. This was both on production and staging (the staging errors were via letsdebug.net). I did not see any of those today; I do not know if that is relevant.