Hi,
First of all, please attempt to upgrade your CTW client to latest version.
Mutli-VA issue, in your case, generally means you didn't give enough time for your DNS provider to propergrate your edits to DNS record across all their server. (So the request of challenge query might be inconsistent, which is an issue after Let's Encrypt enforced mutli-VA)
Which DNS provider did you use? CTW developer said there might be an option for you to set the duration between update your record and request let's Encrypt validation so that your provider will have enough time to propergrate. (I personally suggest to have a duration of at least 2 minutes)
Hope this will clear some confusion..
Thank you