Steve, do you probably have the 'Ignore application processing failures' option selected in Advanced options for Guest processing settings? Veeam AAIP could fail on these VMs for some reason causing Hyper-V guest quiescence to be used and crash-consistent backup option came into play. I would check permissions for the guest OS and Integration Services version.
Also, there is a chance that these VMs could be backed up using saved state only (could be due to Hyper-V Integration Services failure, for example, or if the VM guest OS has dynamic disks). In this case, such VMs will be always backed up in crash consistent mode, regardless of the settings mentioned above.
Anyway, you can contact support directly if you need assistance in identifying the reason of this behavior. Thanks.