What service pack and hotfix you are on?
I have been experiencing the same issue after upgrading to SP16 from SP9. VMWare synthetic full works fine but file server synthetic full throw time out erro during backup operation but it recovers from the error by itself and complete the backup job successfully, but the synttetic full takes too long to complete after the SP16 upgrade.
Did you get to the bottom of the problem?
I logged a ticket with Commvault support and they have been investigating the issue more than a month now.