Multiple Apache virtual hosts causing 'Failed authorization procedure'?

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I'm trying to use LetsEncrypt for the first time but I'm having problems with the verification. I suspect its because I host multiple websites on the same IP, some with SSL (non letsencrypt)

When I try to generate the certificate the verification fails saying it cannot connect to 46.101.174.29:443, which is strange as I can connect locally without any problem.

Could this be because I already host other virtual hosts on the same machine, some with SSL?

My domain is:

I ran this command:
./certbot-auto --apache -d flexlabs.io

It produced this output:
Failed authorization procedure. flexlabs.io (tls-sni-01): urn:acme:error:connection :: The server could not connect to the client to verify the domain :: Failed to connect to 46.101.174.29:443 for TLS-SNI-01 challenge

IMPORTANT NOTES:

  • The following errors were reported by the server:

    Domain: flexlabs.io
    Type: connection
    Detail: Failed to connect to 46.101.174.29:443 for TLS-SNI-01
    challenge

My operating system is (include version):
Ubuntu 14.04

My web server is (include version):
Apache/2.4.7 (Ubuntu)

My hosting provider, if applicable, is:
Digital Ocean

I can login to a root shell on my machine (yes or no, or I don't know):
Yes

I'm using a control panel to manage my site (no, or provide the name and version of the control panel):
No

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