Unfortunately I am not able to replicate your error 
Below is screenshots of challenges passed with ZeroSSL (online client) and Certbot (0.13.0) on Windows
I use 4096 bit RSA keys for my accounts. I have also left the challenge files so you can verify with the domains etc.
This narrows it down to one of 3 possible scenarios
- Key issues (account key)
- Client Implementation Issues
- Incorrect Challenges Being Issued by LetsEncrypt
Not sure where the next steps are @jsha @schoen @bmw any major changes with boulder recently that would cause account keys not to work as expected?
For some reasons the challenge files are not lining up with the keys (i.e. one challenge is being provisioned but not in line with what should be done cryptographically)
ZeroSSL:
Certbot on Windows:
Andrei