This is a quick summary of this problem and discoveries so far. The TLDR version is: This appears to be an OS problem, so I reloaded Windows.
Windows 2008 R2 with B&R 8 patch 3
Examples of errors from the logs:
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[26.01.2016 06:25:00] <01> Error Failed to call RPC function 'FcFindBegin'. InParams: '<InputArguments><SearchMask value="E:\Veeam" /></InputArguments>'.
[26.01.2016 06:25:00] <01> Error [VEEAM02] Failed to create directory 'E:\Veeam' (System.Exception)
[26.01.2016 06:25:00] <01> Error at Veeam.Backup.ProxyProvider.CProxyFileCommander.CreateDir(String dirPath)
[26.01.2016 06:25:00] <01> Error at Veeam.Backup.Core.CBackupRepositoryEx.CreateRootDir()
[26.01.2016 06:25:00] <01> Error Error code: 0x80070008
[26.01.2016 06:25:00] <01> Error Cannot initialize COM runtime
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[31.01.2016 22:28:26] <18> Error Failed to call RPC function 'BeginStopAgent'. InParams: '<InputArguments><agentId value="a41e3d05-c532-4a87-9bca-7c39dc3b6d18" /></InputArguments>'.
[31.01.2016 22:28:26] <18> Error Error code: 0x80070008
[31.01.2016 22:28:26] <18> Error Cannot initialize COM runtime (System.ApplicationException)
[31.01.2016 22:28:26] <18> Error at VeeamProxyClient.RegenerateCLRException(exception* excBase)
[31.01.2016 22:28:26] <18> Error at VeeamProxyClient.CCliProxyRpcInvoker.DoRpc(String cmdName, String inXml, String& outXml)
[31.01.2016 22:28:26] <18> Error at Veeam.Backup.ProxyProvider.CProxyRpcInvoker.Call(String methodName, CProxyInvokeInputArg inputArgs, Boolean secureCall)
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2016/01/26 09:55:55 AM :: Getting VM info from vSphere
2016/01/26 10:00:58 AM :: Error: Timeout to start agent
2016/01/26 10:00:59 AM :: Network traffic verification detected no corrupted blocks
2016/01/26 10:00:59 AM :: Processing finished with errors at 2016/01/26 10:00:59 AM
Only thing that does help is a reboot of the server. However often the first run of the backup will abandon the existing backup chain and start a new full backup in a new directory (would love to know the reason). The only way to prevent this from happening is to edit every single job, recalculate the size and relink the job to the same target (it will generate a warning when you do this). You can also use the relink trick to get your job back onto their original backup chain if a new full backup has been made. First move/delete the duplicates, rescan the repository and edit the jobs. It's possible that you only need to do the relink, I did the size recalculation based on another forum post I'd seen. YMMV.
I also discovered after reloading this server that another Windows 2008 R2 was experiencing the same problem, so it's possible a recent Windows update is to blame. In any event I was planning on moving to 2012 R2 and the Veeam migration procedure is pretty straight forward so no point in spending more time trying to solve this annoying issue on an old OS.