I know that in the past cygwin caused problems: somehow the cygwin make was called and crashed or caused other strange effects.
- Have you installed the software into a folder where you have full access (e.g. C:\Freescale\CW MCU v10.4 as proposed by the installer)? if not, copy/move it there.
- Maybe it makes a difference if you run CW as administator (run as > administrator)
- if this is caused by the mingw32-make: CW is using the one in C:\Freescale\CW MCU v10.4\gnu\bin.
There is an older version of it in that folder: you might give a try and rename the make mingw32-make so it runs the older version.
Hope this helps.