For example: :%!sort -k2,2 results in the buffer being replaced with "-k2,2 not found". That is, the Windows sort command was executed instead of the Cygwin (gnu) sort. This is despite the fact that C:\cygwin\bin is at the beginning of the PATH environment variable. If you open a command prompt window and start gvim from the command line, the Cygwin sort is executed properly.