Hi commrade23,
I just tried exactly what you described, resizing a map to 64x64, then back to 128x128, then to 256x256, clicking the X on the settings window to close and apply these new values. It did work for me. I'm using an editor which is the same version and build date as yours, the only difference is that I'm doing it on Linux. I therefore assume what you describe is a bug in the latest version of the editor. Please edit your first post and make it say 'Bug: Megaglest Editor v1.5.0b3 (built July 03 2010)' so the developers will catch up on it.
Thanks for your report.