Sorry we did not get back here earlier – your dump was invaluable in helping us understand what was going wrong, thank you for taking the trouble to generate one and send it in.
There are a couple of issues here – the first is the fact that the engine is disconnecting, and the second is that when this happens, the Eclipse UI freezes as well and cannot be recovered. While we are still looking into reasons for the former, we have a fix for the latter, if the engine disconnects, it will now recover without you having to hard-reset Eclipse and lose work.
We will follow up shortly with instructions on how you can apply a fix to your current installation.