1)

    I installed a new version of module X but CPAN keeps saying, I have the old version installed

    Most probably you do have the old version installed. This can happen if a module installs itself into a different directory in the @INC path than it was previously installed. This is not really a CPAN.pm problem, you would have the same problem when installing the module manually. The easiest way to prevent this behaviour is to add the argument UNINST=1 to the make install call, and that is why many people add this argument permanently by configuring

      o conf make_install_arg UNINST=1

2)

    So why is UNINST=1 not the default?

    Because there are people who have their precise expectations about who may install where in the @INC path and who uses which @INC array. In fine tuned environments UNINST=1 can cause damage.