After you upgrade to VMware vSphere 4.1 Update 3, a new line is added to virtual machine configuration files (.vmx). The line makes the VM configuration files invalid. As a result, Veeam Backup & Replication jobs fail.
The issue has been resolved in build 126.96.36.199.
For details, see the following Veeam KB article: http://www.veeam.com/kb_articles.html/KB1671