I am seeing this issue as well, Jason, have you received a solution yet from support? However it's only happening on about 1/3 of my systems, and it is also happening on a few of my xp systems. I'm wondering if a complete clean of the agent and reinstall would fix the issue and allow patch to work properly. It seems the agent is going to sleep and unable to respond until we restart the service, force configuration update and send basic inventory, then force patch inventory and patch cycle.
All I can say is it's not designed to work this way and shouldn't be this difficult to get it to work properly.