That shouldn't generally happen. Here's a minimal example for illustration:

foo.pl:
$ENV{FOO} = 'bar';
system 'perl bar.pl';
print `perl bar.pl`;

bar.pl:
print "I got $ENV{FOO}\n";
[download]

When I invoke "perl foo.pl" from my terminal, I get:

I got bar
I got bar

So maybe what you're actually seeing is something different? Perhaps a bit of code would help.