OK, attempted to re-install, cpan says all is well and I still have the same problem, now what?
cpan install pp
Set up gcc environment - 3.4.5 (mingw-vista special r3)
CPAN: Term::ANSIColor loaded ok (v3.02)
CPAN: Storable loaded ok (v2.34)
Database was generated on Wed, 27 Feb 2013 12:08:03 GMT
CPAN: Module::CoreList loaded ok (v2.77)
pp is up to date (0.992).
pp -o hello.exe hello.pl
No Perl script found in input
pp still works fine if I move the Perl script into \Perl\site\lib and run the command from there.