Might be a bit of a long shot, but do you keep the combined map on screen at all times? if not what happens if you click the "C" logo? I ask because if they just disappear, it sounds like to me that you have hidden the combined minimap. If clicking the "c" dont work, try to just press "m" twice and see if the buttons show back up
edit: a screen shot could help lots in terms of what your seeing and what we think your seeing
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