We are running Veeam Backup and Replication 6.5 to backup our VMWare environment and also using it to replicate our VMs to our DR site for Disaster Recovery. We had recently been noticing a slow down on some of our VMs, especially during the Processing Configuration step; most of our VMs were completing this step in 10-30 seconds, we noticed some were taking 60+ minutes to complete. After doing some investigation and reaching out to Veeam Support we discovered that you must manually map the Resource Pool and Datastores for each replica VM otherwise the long processing delay will occur. I was surprised at how easily this is overlooked in the GUI; it appears many others miss this as well. (http://blog.mwpreston.net/2013/02/07/veeam-job-taking-a-crazy-long-time-on-processing-configuration-check-your-destination) You must click the 2 blue links: Pick Resource Pool and Pick Datastore. Once you define the locations of the Resource Pool and Datastores the processing configuration step will occur much quicker.
After properly mapping each of our VMs to their resource pool and datastores we noticed a substantial difference in the processing configuration step.
Remember to check in your datastores; Veeam will create a ton of empty VMNAME-replica-# folders in the datastores in which your VM does not reside and should be cleaned out for good housekeeping purposes!
Sure would be nice if they would automate this process thus allowing Veeam to determine the datastore and automatically set these settings!