You might be running into variable persistance. If your variables are globally scoped, they'll hold their values between page loads.

Another common problem is declaring a lexically scoped variable and then trying to use it in a subroutine, e.g.

my $foo = "bar";

sub foo
{
    # It's ok to use $foo here in a normal script,
    # but it may have strange results under mod_perl
    print $foo;
}
[download]

Here is a more detailed explanation.

Post the relevant section of code, and we can probably help you out.

-Matt