I don't know if this issue is still around, but back when SEP first came out one of my SEPM servers had the SEP client installed on it. The Live Update settings for the client seems to override the Live Update settings for the SEPM. In my example I had clients checking our internal Live Update servers at a certain frequency and my SEPM checking at a different one. When I looked at the logs the SEPM server was using the client's Live Update frequency.
Just something to keep an eye on especially if your SEP client Live Update settings differ from what you want for SEPM Live Update settings.
Jeff