We have Windows 2008 server as our centralized storage. All the render machines have the shared folders mapped correctly with all the permissions set. We are using After Effects CS5. What we are finding is that after a few comps have been rendered in a multi-comp project, some will drop off the render queue. What happens is that the render window list disappears and the watch window pops up and keeps cycling as if it's 'lost' the project is supposed to render. Usually, if we reboot or restart the render engine and go back to the watch folder, it "might" pick up the project and carry on rendering. All the machines are on Windows 7 64-bit.
This is a known state, but not directly AE's fault - one of your machines is not able to access footage items within a specific limit and this effectively also shuts down other machines because they, too, go into this waiting forever state. Ultimately it boils down to too many machines trying to access the same files or directories and clogging up your network. The only way to avoid it is to ramp up your network bandwidth or e.g. instead of working with compound movie clips, work with image sequences.