Update;
First, I was wrong about the NICs in the HTPCs, they are both using nForce NICs which might explain why those back ups rarely fail. The desktop is using a RealTek NIC. I checked that all the settings were as advised above and it still did not fix the issue of losing connectivity to the networked drives. After putting the system to sleep for several minutes and waking it back up again, the connectivity was lost, only a restart got the network drives back up.
So I think I’ll go shopping for a NIC.
