I think you're experiencing this issue https://github.com/SignalR/SignalR/pull/1553. We're working on a fix for it. The issue happens when the server sent events request times out but the actual http requests is still going. What then happens is that the longpolling transport and server sent events http requests fight for the connection.
To workaround this you can specify the LongPollingTransport specifically. We'll look at fixing this for the next release.