I was wondering the same thing, so I tried all kinds of things tonight with running as administrator, moving the tool to be on the same drive, opening new projects, opening old projects, trying with new terrains, and trying with old terrains. It worked once out of about 8 permutations and I have no idea why that one worked while all the others fail.
All my tries keep working consistently, I just can't reproduce it. Keep in mind that the tool itself isn't that complicated. It's barely 50 lines of code. It just reads two files and rewrites one of them.
All the code is in two files
https://github.com/Celludriel/DOS_Terrain_Importer/tree/master/DosTerrainImporter/Importer/Dos2Dos2GrayScaleImporter.cs: figures out the name of the patch files and order
PatchFileWriter.cs: reads and writes one patch file
Wish I could reproduce your problem, but I get consistent results
