Much of the above seems to be irrelevant now.
After posting in the OWIN JabbR room, a solution to the problem seemed to be either:
Configuring SignalR BEFORE WebAPI:
or mapping the SignalR and Web API like:
app.Map("/api", (b) => ConfigureWebAPI(b));
app.Map("/signalr", (b) => ConfigureSignalR(b));
Quite what this indicates, I'm not sure. However it does fix my issue.