The issue might be you added an inventory item to a critter that cannot use that item. It is better to build your maps in stages (incrementally), and place any items at the very end…wrong items have been known to screw the maps completely.
Try to download Dim’s Mapper here at NMA and see if it can open the fore mentioned maps, and remove any questionable items. Re installing won’t fix the maps – and remember to build the maps clean of critters and items – then save the files with a new name before adding the finishing touches… (Also beware – Dims Mapper is not 100% stable).
To be honest, this sounds like a proto problem. Did you edited any proto file in mapper? Critters, items? You wrote above, that you didn't add anything, but maybe you have done this by accident?
(if you had turned the save map as text in the cfg) You could try copying manually your map levels to a different newly made map that way there is a chance you can save some of your work. http://falloutmods.wikia.com/wiki/Merging_maps