Sometimes I come across maps sitting on tables, covered with green and red flags indicating imperial or stormcloak possession. You can activate the maps and it tells you "Map updated." But my question is, what exactly was added or changed? And do all the table maps update the same things? Thanks!

My guess would be it adds an Imperial or Stormcloak Camp marker to your map. The Stormcloak camps are a bearclaw symbol, the Imperials are the Diamond Dragon symbol from the main screen,

It also adds any forts, towns or other locations held by one of those factions.

Plus each map is a little different. Some of the smaller locations change depending on which factions map it is. ie: A Stormcloak map may have a couple of of their positions, but lack a couple of locations that you'd find on an Imperial map.