After creating new analytics accounts for 8 mini-sites (they were previously tracking on old accounts) we updated the UA code in the plugin settings. However Google was reporting that tracking was not enabled. I couldn't see anything unusual with the setup so I turned on debugging. In firebug, I saw that '_trackPageLoadTime' is deprecated. I disabled Site Speed tracking and the 8 sites began to record data.
I don't know if the above is just a coincidence but I thought it would be good to describe it anyway.
Thanks for a great plugin.