We are using an internal certificate on our server and I\'ve followed the steps in
https://blogs.msdn.microsoft.com/tfssetup/2016/12/19/error-ssl-certificate-problem-una
Since you can't manually using the build agent account to run the command. Please double check if you or your mates ever modified the permission for "Project Collection Build Service" account. If you do not have, please add one.
Also confirm your build agent version, make sure have updated to the latest. You could use another new build agent instead of this one to narrow down the issue.
If above couldn't figured out the issue, you may need some more diagnostic info such as give a Fiddler trace.