Very strange. Is this a responsive project? Perhaps the LMS sets the window size and the responsive project is moving the buttons outside the slide area.
If it's SWF output, I can't imagine why this would happen. Go back to the project and preview it in browser (F12). Check that "Visible in output" is turned on for each button (the little eye next to the name in the properties tab) and that the buttons are timed correctly on the timeline.
That's all I can think of right now. Best of luck!