Version: Modkit 1.0.4 Beta Build 140825 (initial release) OS: Tested on Windows 7 and 8.1
If the modkit installation directory contains a dot ("."), the "bin\Tools-x64.exe /mod" command will create a .crs file but silently fail to create a .pkm file. This affects all mods including the examples.
This is likely to affect many users who re-use the archive file name ("BanishedKit_1.0.4.Beta.zip") as their installation directory.
It happens with any non alpha-numeric characters in the path. Even when I used underscores, I got mysterious and hard to diagnose errors during builds. This stumped me for a couple of days honestly.
Making the path contain only letters is what magically fixed it.