I have the exact same error after closing and reopening a project with two routers and two switches. After reopening, the switches did not appear.
O/S: Windows 8.1 x64
GNS3 server version 1.0beta1
Copyright (c) 2007-2014 GNS3 Technologies Inc.
Running with Python 3.3.5 and has PID 9312
[W 140730 20:50:21 __init__:79] vboxwrapper couldn't be found!
[I 140730 20:50:21 server:223] ZeroMQ server listening to 127.0.0.1:51722
Starting server on 127.0.0.1:8000 (Tornado v3.2, PyZMQ v14.2.0, ZMQ v4.0.4)
[I 140730 20:50:21 jsonrpc_websocket:118] Websocket client 9ac436df-8471-4bf6-8117-eab821961413 connected
[I 140730 20:50:21 web:1728] 200 GET /version (127.0.0.1) 1.00ms
[EDIT]
Just read this note
topic11132.html which seems to acknowledge the error. I did delete some of the default Ethernet switch ports.