This is typical behavior.

On most systems, the routing of each packet is determined when the
packet is about to be sent. Just because it comes in a NIC, does't mean
it will response will respond through the same NIC.

Since you have multiple interfaces to the same logical network, the
determination of which on it will be sent out, will be determined by
anyone of multiple factors. The instance number of the NICs. The IP
addresses of the network interfaces. Order of routing table entries.
The only way to be sure is to peruse the source code. 

Does this mean my best bet would be to put the backup NIC on another VLAN? - at 
least until I can work out if the network is, or is one of, the reasons for my 
poor backup performance.

Cheers
John

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