Backups from Storage Snapshots should wait for all vm snapshots in the same volume in the same job to be completed, are all the vm in one job?
There are also limits on the number of snapshots per ESXi and datastore that can be taken concurrently, but then what's in the queue should wait.
You can try to disable the Failover to nbd in the proxy settings and see if it changes the behavior.
EMEA Cloud Architect @ Veeam Software
Veeam VMCE #1