Nuno and Rob,I came across this problem with ESX few times but not with windows yet. but Rob is correct. This is hashing algorithem issue on host side. On ESX, the only one is compatiable with cisco port-channel is ip based hashing. What NIC teaming ...
If you are sure control, packet vlan have configured correctly, then you can try to remove that host from dvs and add back in. It is better to choose the vmnic when you add the host to the N1K rather than adding it later. N1K needs at least one vmnic...
How many uplink port do you have per each switch?Try channel-group auto mode on mac-pining instead sub-grup cdp.Make sure you don't configured port-channel on uplink switch when you use mac-pining.