When the network connection between the controller and the switch is not stable, flow mods attempted to get installed from the controller may not go on the wire, but the message from UI says: "The failure is: Failed to add the flow: Request Timed Out". This is not clear.

For example:
2013-05-15 11:18:18.420 PDT [http-bio-8080-exec-5] WARN o.o.c.f.i.ForwardingRulesManagerImpl - SDN Plugin failed to program the flow: FlowEntry[flowName = Marvell Test 1, groupName = **StaticFlows,node = OF|00:00:02:5f:b8:47:63:c9, flow = Flow[match = Match[[DL_TYPE(2048,null), IN_PORT(OF|7@OF|00:00:02:5f:b8:47:63:c9,null)]], actions = [DROP], priority = 123, id = 0, idleTimeout = 0, hardTimeout = 0]]. The failure is: Failed to add the flow: Request Timed Out

On controller side the issue I see is that SwitchHandler.syncMessageInternal(…) catches on the generic Exception and assumes it is always because of switch barrier reply timeout…
With a more granular catching, the proper error message could be returned and save debug time…