Same problem here, for all my domains (served with apache).
Exemple:
2015-12-04 17:28:52,367:INFO:requests.packages.urllib3.connectionpool:Starting new HTTPS connection (1): acme-v01.api.letsencrypt.org
2015-12-04 17:28:52,595:DEBUG:requests.packages.urllib3.connectionpool:"POST /acme/new-authz HTTP/1.1" 201 568
2015-12-04 17:28:52,597:DEBUG:root:Received <Response [201]>. Headers: {'Content-Length': '568', 'Expires': 'Fri, 04 Dec 2015 17:28:52 GMT', 'Strict-Transport-Security': 'max-age=604800', 'Server': 'nginx', 'Connection': 'keep-alive', 'Link': '<https://acme-v01.api.letsencrypt.org/acme/new-cert>;rel="next"', 'Location': 'https://acme-v01.api.letsencrypt.org/acme/authz/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE', 'Pragma': 'no-cache', 'Cache-Control': 'max-age=0, no-cache, no-store', 'Date': 'Fri, 04 Dec 2015 17:28:52 GMT', 'X-Frame-Options': 'DENY', 'Content-Type': 'application/json', 'Replay-Nonce': 'nhy4joMFJCGdANEnam_VX6kFLJt4Ki-OOYSqud-TIPA'}. Content: '{"identifier":{"type":"dns","value":"damien.clauzel.eu"},"status":"pending","expires":"2015-12-11T17:28:52.514553153Z","challenges":[{"type":"tls-sni-01","status":"pending","uri":"https://acme-v01.api.letsencrypt.org/acme/challenge/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE/798523","token":"xjWCCltlo67PhGyRntiUg1OkaFfSx0yQti05465CH0Y"},{"type":"http-01","status":"pending","uri":"https://acme-v01.api.letsencrypt.org/acme/challenge/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE/798524","token":"5j3MGPF8BIGUI99as4gTcUs7wjuTVrGroxq5iJB4jRg"}],"combinations":[[0],[1]]}'
2015-12-04 17:28:52,598:DEBUG:acme.client:Storing nonce: "\x9e\x1c\xb8\x8e\x83\x05$!\x9d\x00\xd1'jo\xd5_\xa9\x05,\x9bx*/\x8e9\x84\xaa\xb9\xdf\x93 \xf0"
2015-12-04 17:28:52,598:DEBUG:acme.client:Received response <Response [201]> (headers: {'Content-Length': '568', 'Expires': 'Fri, 04 Dec 2015 17:28:52 GMT', 'Strict-Transport-Security': 'max-age=604800', 'Server': 'nginx', 'Connection': 'keep-alive', 'Link': '<https://acme-v01.api.letsencrypt.org/acme/new-cert>;rel="next"', 'Location': 'https://acme-v01.api.letsencrypt.org/acme/authz/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE', 'Pragma': 'no-cache', 'Cache-Control': 'max-age=0, no-cache, no-store', 'Date': 'Fri, 04 Dec 2015 17:28:52 GMT', 'X-Frame-Options': 'DENY', 'Content-Type': 'application/json', 'Replay-Nonce': 'nhy4joMFJCGdANEnam_VX6kFLJt4Ki-OOYSqud-TIPA'}): '{"identifier":{"type":"dns","value":"damien.clauzel.eu"},"status":"pending","expires":"2015-12-11T17:28:52.514553153Z","challenges":[{"type":"tls-sni-01","status":"pending","uri":"https://acme-v01.api.letsencrypt.org/acme/challenge/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE/798523","token":"xjWCCltlo67PhGyRntiUg1OkaFfSx0yQti05465CH0Y"},{"type":"http-01","status":"pending","uri":"https://acme-v01.api.letsencrypt.org/acme/challenge/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE/798524","token":"5j3MGPF8BIGUI99as4gTcUs7wjuTVrGroxq5iJB4jRg"}],"combinations":[[0],[1]]}'
2015-12-04 17:28:52,600:DEBUG:letsencrypt.cli:Exiting abnormally:
Traceback (most recent call last):
File "/root/.local/share/letsencrypt/bin/letsencrypt", line 11, in <module>
sys.exit(main())
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/cli.py", line 1283, in main
return args.func(args, config, plugins)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/cli.py", line 512, in obtain_cert
_auth_from_domains(le_client, config, domains)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/cli.py", line 336, in _auth_from_domains
lineage = le_client.obtain_and_enroll_certificate(domains)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/client.py", line 283, in obtain_and_enroll_certificate
certr, chain, key, _ = self.obtain_certificate(domains)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/client.py", line 266, in obtain_certificate
return self._obtain_certificate(domains, csr) + (key, csr)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/client.py", line 224, in _obtain_certificate
authzr = self.auth_handler.get_authorizations(domains)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/auth_handler.py", line 74, in get_authorizations
domain, self.account.regr.new_authzr_uri)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 215, in request_domain_challenges
typ=messages.IDENTIFIER_FQDN, value=domain), new_authz_uri)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 198, in request_challenges
return self._authzr_from_response(response, identifier)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 179, in _authzr_from_response
raise errors.UnexpectedUpdate(authzr)
UnexpectedUpdate: AuthorizationResource(body=Authorization(status=Status(pending), challenges=(ChallengeBody(chall=TLSSNI01(token='\xc65\x82\n[e\xa3\xae\xcf\x84l\x91\x9e\xd8\x94\x83S\xa4hW\xd2\xc7L\x90\xb6-9\xe3\xaeB\x1fF'), status=Status(pending), validated=None, uri=u'https://acme-v01.api.letsencrypt.org/acme/challenge/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE/798523', error=None), ChallengeBody(chall=HTTP01(token='\xe6=\xcc\x18\xf1|\x04\x81\x94#\xdfZ\xb3\x88\x13qK;\xc2;\x93V\xb1\xab\xa3\x1a\xb9\x88\x90x\x8d\x18'), status=Status(pending), validated=None, uri=u'https://acme-v01.api.letsencrypt.org/acme/challenge/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE/798524', error=None)), identifier=Identifier(typ=IdentifierType(dns), value=u'damien.clauzel.eu'), expires=datetime.datetime(2015, 12, 11, 17, 28, 52, 514553, tzinfo=<UTC>), combinations=((0,), (1,))), new_cert_uri='https://acme-v01.api.letsencrypt.org/acme/new-cert', uri='https://acme-v01.api.letsencrypt.org/acme/authz/S5-JE4rNYkF5nN4i3WelgLl5kdJGTQcCs41rnvpHPyE')