The mapserver is generally believed to be the same thing as the server, only called by its internal name in the warning messages regarding it. The most common message regarding the mapserver is "Lost connection to mapserver", when the game's client and NCsoft's servers stop communicating properly, generally due to excessive lag. It is possible to recover from a mapserve and continue playing, but sometimes the player is kicked offline. Players refer to this as being mapserved.
During the Dual Pistols Beta on the Training Room, a bug occured in which certain zones were thinking that the time was four hours off of what it was. One of the devs mentioned on the official forums (unable to find/link to the post, as old beta notes seem to be deleted/locked) that this was because a single mapserver had had its time set incorrectly. They stated something to the effect that for each server (e.g. Freedom, Virtue, etc.) there are multiple mapservers, and whenever a zone is first entered, it is assigned to a mapserver (this includes city/hazard/etc. zones like Atlas Park or Steel Canyon, as well as instanced zones for missions). If the zone is emptied, it is removed from the mapserver, and, in the case of persistent zones, re-created on any mapserver (maybe the same one, maybe not) when somone enters it again. Also, this means that if a zone fills to the point of duplication (Atlas Park 1 and Atlas Park 2 exist, for example), they are probably not going to be on the same mapserver, for load balancing reasons, and it explains why the extra copy of the zone automatically disappears when emptied - that zone is removed from its mapserver, leaving only one copy.