Okay, *THAT* is a problem, I've never had that happen to me.

The only time I get a long wait is when I'm adding a new season pass or modifying an existing one so that it's gotta go sift through its database and re-prioritize. The more season passes I have on the box, the slower it operates during database scrapes.

Unless you've got a mind-boggling number of season passes and items in there, I would be suspicious of something wrong. It should never miss the first minute of a show unless the show genuinely started a minute too early.