Let's Encript SSL Certificate and Azure Traffic Manager

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I am trying to use Azure Traffic Manager to load balance traffic between a website hosted on an Azure VM in 2 different regions (Europe and US).

The Azure Traffic Manager is setup happily with the DNS name mywebsite.trafficmanager.net

I have 2 end points setup with dns names mywebsite-uk.uksouth.cloudapp.azure.com and mywebsite-us.westus.cloudapp.azure.com

In order to setup a vanity domain I have a CNAME record pointing to

www.mywebsite.trafficmanager.net

When I go to http://mywebsite.trafficmanager.net or www.mydomain.com I get correctly routed to the closest site.

Unfortunately I am struggling when I try to get HTTPS / SSL working. I am attempting to use Let's Encrypt via the Certify SSL Certificate Management tool to issue an SSL certificate to each of the servers however I am getting the following error:

Validation of the required challengers did not complete successfully. Please ensure all domains to be referenced in the Certificate can be used to access this site without redirection.

I have created bindings in IIS for both mywebsite-uk.mydomain.com and www.mydomain.com, and an A record for mywebsite-uk to the ip of the web server and whenever I request a certificate that includes www.mydomain.com I get the error.

Has anyone got an experience with this type of setup? and more importantly any advice on what I am doing wrong? Would I be better biting the bullet and getting a paid for SSL certificate?

Many thanks in advance,

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