I've regressed to a previous firmware and it appears the shares don't just mysteriously drop off any more. I'm pretty sure this is a fault of the ReadyNAS 4.2.12 firmware.

With regards to the initial issue I mentioned, about restarting the NAS, I'd love to try out the program if you can dig it up. At the very least it should stop any Windows software that doesn't cause the shares to be remounted not to fail. I'm pretty sure SageTV, my PVR software, still has it's own issue here as well though.