Assuming you did attatch the condenser (securely), here are two possible causes:
1. You heated it too hard. Before leaving the reaction unattended make sure your oil bath has been on a constant setting for at least half an hour and check with a thermometer so you can be sure your oil bath has stopped warming up, and check that that no vapours are escaping (you can see the vapours condensing in the condenser, make sure this is occuring no more than half way up the condenser, just to be sure). The temperature dial on oil baths is rarely reliable, so you need to make sure it has reached a constant appropriate temperature before you leave the lab.
2. Loss of water pressure. Make sure the water flow in your condenser is fast, because the water pressure in the plumbing system will probably be subject to fluctuations - this has happened to me before with the same result you experienced, I came back after lunch once, flow had dropped considerably and the ether was gone!
Just make sure you double check it all before you leave and it should be fine. I've refluxed reactions in acetone overnight a fair few times now without problems.