Unfortunately, it is common for cert providers to provide the wrong intermediate certs when they provide you with a chain. I have run across this many times.
1) You will need to look at the specific cert and look for the Issuers Certificate Common Name and then try and hunt through and find the one it's looking for. They may have cross-signed a certificate to make it valid to browsers, but the VCS won't do that. It wants the actual signed intermediate.
2) Make sure you upload them in the right order. If you upload them out of order, the VCS won't validate it even if the right cert is in the list.
