I guess MKS runs its own config scripts at cmd.exe startup or windows startup somewhere (not sure)
That's an abominable state of affairs !! Is perl itself crippled by this affliction ?
For example, does perl -e "print $^X" output C:Perl64perlbinperl.exe, or is it just the cpan shell that suffers ?
If the problem is limited to the cpan shell you might be able to work around the problem by simply not using it.
I *never* use the cpan shell - in fact I won't even use cpan.pm (or any of its variants) unless the module I'm trying to install has an appallingly long list of pre-requisites.
In reply to Re^3: cpan fails when MKS installed on Windows