The precise location determined by PREFIX depends upon perl's configuration. Perhaps the new perl has been configured slightly differently, and it's that difference that accounts for the change to PREFIX.

Best way to avoid problems like this is to:

perl Makefile.PL INSTALL_BASE=/mylocal/path
[download]

I don't know whether that will put modules in the same place as the old PREFIX did, but it will not be dependent upon perl's configuration, and will remain the same from one build of perl to the next.

For further info, see the ExtUtils::MakeMaker documentation. (See the "INSTALL_BASE" and "PREFIX and LIB attribute" sections.)

Cheers,
Rob