(trying this against systems currently at my fingers, my linux boxes are at home)

Perhaps it's different on Linux, but on Aix(perl 5.8.0) and Solaris 2.6(perl 5.6.1)

$ENV{FOO}='bar' ;
system('echo $FOO') ;
[download]

produced:
bar

On Win2k(perl 5.6.1) you have to change $FOO to %FOO% but you get the same result.

This suggests to me that the environment is getting altered and picked up the the child processes of the perl script.