I will randomly guess that MKS Toolkit along with Interix were written using Native API and both had full access to the Windows source code from Microsoft (read the story about Mainsoft), therefore both are faster and cleaner than Cygwin which was written on top of Win32 without detailed knowledge of Windows NT.

In reply to Re^2: cpan fails when MKS installed on Windows by bulk88
in thread [Solved]: cpan fails when MKS installed on Windows by prashantktyagi

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