When "minimizing" the player from a button on the Control panel (or 'main window') BSPlayer's "Tray icon" (as defined at the bottom right of "General"-tab in preferences) is placed in the System tray (bottom right of the PC window).
From there BSPlayer's control panel can be reactivated by double clicking on it. (This only functions if a video-file is loaded.)
So what you call "minimizing" is actually a different function. BSPlayer is exactly doing what it is expected to do. The movie window is supposed to stay open. However BSPlayer is moved from the Taskbar to the System tray.
Perhaps the control-panel's skin is confusing you as it may use for this BSPlayer-function an icon similar to Window's "minimize"-instruction. This - of course - can vary with the skin used for BSPlayer.
When you are minimizing from the taskbar, you're using the Windows function, which indeed closes both main window and video window, leaving BSPlayer on the taskbar.