I'm playing on a mac and on the internet that I currently use I get bumped from the net every 30 minutes or so. This seems to cause me to be unable to do things for a while. My health goes down as I get hit by monsters I can't see. This will go on till I die or logoff. If I'm not in combat while this happens, or if I survive combat, I can communicate with others after the spike but the game seems hung up on everything else.
If I relog I'll end up in Haven when I come back which is kind of a bummer.
Is there a way to shut off the client and restart and still be in the dungeon?
Usually when you get disconnected you eventually get returned to the the log-on screen. If you don't restart your client you can pick up more or less where you left off. It sounds like you're reconnecting before this has a chance to occur.
Does this happen with any other game or just Spiral Knights? Either way I'd recommend you run a Java update if you haven't already done so.