Do you have Wireshark, and either an old-fashioned hub or a switch/router which will copy all packets to all ports? The easiest way to debug the networking traffic-on-the-wire side of this is by using Wireshark.
Is there any special action you take based on packets received after the start of a new hour? Extra threads (or blocking threads) that happen on that hour marker? Networking does live at the managed code layer--so if there's a blocked thread within an event handler...NETMF may not be so happy to let network traffic through.
This is a very curious issue, very interesting. Let's figure it out.

Chris