There were couple of common issues reported by customers who had applied Veeam Backup & Replication vSphere 5 compatibility patch which can both result in reduced job performance, so I wanted to give you heads up.
Most customers choose to upgrade to vSphere 5 along with applying said B&R patch. However, it seems that certain strategies our customers employ to move VMs to vSphere 5 brake CBT data on some VMs. Veeam B&R detects CBT data inconsistency, and fails over to legacy "snap&scan" method of determining incremental changes, which is noticeably slower than CBT (as it requires whole VM image to be read). From user pespective, this translates into very slow incremental backups. To fix CBT on affected VM, use vSphere Client to edit advanced VM setting and set all parameters with CTK letters to false. This will reset CBT, and our job will then automatically enable it on each processed VM.
Also, under certain circumstances, the patched B&R data mover agent may exhibit increased CPU usage. In cases when B&R server lacks available CPU resources, this increase makes CPU to become a bottleneck, which in turn reduces the overall processing performance. We now have the new agent version available through our support addressing this problem. If you don't have unusually high CPU load on your B&R server after vSphere 5 patch (for example, hotadd mode is not affected by this), then you do not need to install the new agent, as it does not change anything else.