If I compare the SHA-1 shown for the certificate for https://0000.jp in Chrome:
79 72 28 12 74 83 85 DE 3C B0 DE E7 A4 C3 14 BE B4 93 79 6E
with that presented by OpenSSL:
$ echo -n | openssl s_client -connect 0000.jp:443 2>/dev/null | openssl x509 -noout -fingerprint
SHA1 Fingerprint=79:72:28:12:74:83:85:DE:3C:B0:DE:E7:A4:C3:14:BE:B4:93:79:6E
then I get the same value.
If I do the same for https://google.co.uk then Chrome shows:
06 4B 11 0D 63 4A 83 E2 6B 1A 12 19 EC 04 46 F3 7C 3A 01 D7
while OpenSSL shows:
$ echo -n | openssl s_client -connect google.co.uk:443 2>/dev/null | openssl x509 -noout -fingerprint
SHA1 Fingerprint=3F:6D:D9:AB:60:92:1E:EE:D3:4C:C7:36:04:49:B2:FA:F9:E5:2D:92
There are no warnings in Chrome and I'm assuming the NSA/Russians/North Korea aren't as likely responsible as an error on my part... so what's the reason for the difference?