I can't explain the why as I am sure it is just an issue interfacing between SL and the website, but I have seen what you mention happen. I have 2 or 3 friends on my SL friend's list that often don't show on the list on the website. If they are online in SL then they show up on the website friends online, but when they are offline in SL they may appear as offline on the friends online or there names might not even show up on the list at all. The 1st time this happened I thought someone had either removed me as a friend or quit SL, then when I logged on to SL later I was glad to see that they were still on SL and still a friend. I guess you just have to use friend's online on the website and keep in mind that it might not be exactly what you'd see in SL.