When you asked this in the chatterbox, you should have mentioned "5.003", because then you would have gotten an answer. None of us realized you were talking about such an antique.

http://search.cpan.org/grep?release=perl5.003_07&string=EMBED&n=1

Which mostly points to Changes5.003 which says:

The EMBED namespace changes are now used by default, in order to better segregate Perl's C global symbols from those belonging to embedding applications or to libraries. This makes it necessary to rebuild dynamic extensions built under previous versions of Perl without the EMBED option. The default use of EMBED can be overridden by placing -DNO_EMBED on the cc command line.

The EMBED change is the beginning of a general cleanup of C global symbols used by Perl, so binary compatibility with previously compiled dynamic extensions may be broken again in the next few releases.