Media Player only seems to scan directory contents when descending into a folder from its parent. It displays cached data when finishing playing a video or when ascending from a child. This means that the on-screen display is wrong for me the most of the time, since files are frequently being added and removed on my server.
The workaround is to always hit menu to go up a level, then reselect the folder to force a rescan. It’s a pain, though. Really, any time it’s going to display a folder’s contents, it should rescan to ensure that it is showing accurate contents at that moment.