The Perl::Dist and Perl::Dist::Bootstrap test suites builds an entire test distribution in the tests.
A problem with the way "make test" sets PERL5LIB inside a test that is itself running inside a "make install" results in a problem where modules from the child make install are installed to the location configured for the outside make test.
In short, Perl::Dist installs stuff over the top of your main Perl distribution.
Andreas has pro-actively (and correctly) removed all the new developer versions of Perl::Dist to prevent damage to the CPAN Testers (and any others playing with it).
It's taken three days to get to the bottom of the exact problem, but now inside the tests it will pro-actively reset PERL5LIB to a null string every time it calls any child process.
This not only appears to fix that bug, but in the process of trying to make child process calls cleaner, also fixed a whole bunch of other bugs as well.
As a result, I think I now have phase 4 (installation of modules via the CPAN client) working cleanly as well.
This leaves one only phase 5 to finish (the generation of the .exe installer itself) before I can release Bootstrap Perl (and from there the new Vanilla/Strawberry Perl).
I think I can see the light at the end of the grindy grindy tunnel.