In Megaton Edition, many maps are patched to fix minor bugs. This usually doesn't have a noticeable effect on speedrunning, but in Nuclear Winter, certain skips are made impossible by these patches. Fortunately, the original map files still exist within Megaton Edition, and can easily be restored:

1. Go to Steam/steamapps/common/Duke Nukem 3D/gameroot/addons/nw

2. Move all of the .MAP files out of the folder, to wherever else you like

Now, instead of reading the patched .MAP files, Megaton will instead read the .GRP file, which contains the unpatched maps.