I am having the same issue, with a twist: On my Cisco C3560-CX 12PD-CS, latest IOS 15.2.7, with a very similar configuration
a) If I send the enrollment request using "terminal", the signature algorithm used is sha256, as specified by the "hash sha256" configuration command
b) If I send the enrollment via URL TFTP, the signature algorithm is *always* MD5, i.e. "md5WithRSAEncryption", something which my CA (resp. openssl) refuses to accept.
So, I am very interested if you have received any answer from other people, or Cisco ? Or could you find a fix for that ?
PS: We don't have any support for these C3560 anymore, and because they are very much EOL, Cisco (on another occasion) was very coy of providing TAC support.