I am also having this issue. Machines, and Windows processes and services show unavailable and send out an alert, then randomly, they all appear back up. Meanwhile the server itself was running fine.
We are also seeing the little bursts of unavailability reported by Ralf. If one RESOURCE for a machine is showing unavailable, usually all of them are unavailable for that machine. If one MACHINE shows unavailable, typically all machines are showing unavailable, but not always. As Ralf noted, it doesn't seem to be an issue with time synchronization, our machine's are synchronized. This seems to happen regardless of the load or traffic on the client. In fact it is also happening to our initial test client which is currently doing nothing but running Windows and the Hyperic agent.
While the resource is showing unavailable, we can still execute queries against the resource in Live Exec, there is no delay in the results it shows. I've been testing several scenarios and haven't seen any evidence that there is an issue with communication, and obviously if we can query with Live Exec, it is capable of communication with the client while this is happening in HQ. It's very odd...
Our servers are Windows 2003, 2000, fedora and some XP with no virtualization.
We am using version 4.5, a fresh first-time install.