I tried making a custom map but was unable to do so. When I try to play the map I just saved, it instead seems to be a completely new random map. I then went back and made a few test maps to reproduce the problem and got the same result. The problem should be readily made by anyone and I am interested to see if it's just me or if others have the issue as well. To do so, make a random custom map, save it, then try loading the map up. Should come up as completely different terrain.
An additional but separate issue is that the delete map button doesn't seem to work as well within the save map menu in the cartographer's table.