Hey Jake,
Me and AG both have cases open with VMware about this. This issue have been going on for few months now since the upgrade to 5.1 version.
We have looked at the datastores, and networking and ruled those out as problem areas strictly because they did not have any problems.
I even went to the extend as deploying a brand new Cisco switch configuring it for my management network and connecting all the hosts there and the issue still remains when the vcenter will report a host as disconnected/unavailable.
I ran a wireshark on one of the interfaces on that switch to capture traffic as this is happening but with my luck this event did not accour for few days of the wireshark running.
Hope the thread that me and AG have going on this can help you identify the issues soon as the solution is found.
thanks.