For example, in the case of XML::Generator, version 0.90 is a single file that just needs to be copied into the appropriate location. Version 0.91 works fine, but fails "make test" out of the box (I think it has an undeclared dependency on XML::DOM) and thus won't install using CPAN.pm. Also, extremely early versions of XML::Generator were distributed bundled with other XML tools, and could cause library-path problems. It'd be much simpler if we just stuck Generator.pm in an appropriate directory and required it using an absolute path.
That's an extreme case, but any module we rely on is a potential source of trouble if a later version breaks back-compatibility in some way, or breaks the installer. Might as well dodge it when possible. (When possible == when it doesn't need to be compiled, when it's a relatively small number of files, etc.)
Candidates for such inclusion: Time::DaysInMonth, XML::Generator, Class::Singleton, MIME::Lite, Image::Size, HTML::Tagset, maybe GD::Text and GD::Graph.