I have a support case on this (Case # 01092404), but thought I would share.
I have one physical box running VM 5.10 as the host with 5 Windows guests (A,B,C,D,E). All the guests use a common datastore, "DS1". One guest is disabled, so only 4 vm guests are backed up: A,B,C,D. (VBR runs on a separate physical, dedicated server. ) "E" is specifically excluded in VBR backup job. One VBR task runs every night to back up the host and has worked fine for years. Since "E" is excluded (and has been for 2 months), only A,B,C,D are backed up these days. Great.
I added an NAS last week for temporary, duplicate file storage as I am preparing to relocate data. I assigned the NAS to guest "C" and I don't need to backup the NAS, so I asked VBR to exclude the NAS ('DS2" datastore), but otherwise carry on as always. I did NOT exclude the vm guest "C", JUST excluded the NAS.
VBR casually excluded guest "C" completely which I did not notice for 4 days. A,B,D backed up perfectly fine as always. I was shocked by C's exclusion once I finally noticed its absence from the VBR log (note to self - read all the VBR email detail - it did not mention C at all which is a clue). Since "C" is both the domain controller and has an abundance of critical project information on it, well..... thank god I finally noticed.
Guest "C" o/s is 'running' on DS1, and not the excluded NAS -- "C" just uses the NAS for supplementary storage. Weird that it was excluded. For today, I removed the exclusion to the NAS to get a full backup. Once complete, I will try excluding "drives" instead of excluding the secondary datastore.