That is because in sub stoptime, your script doesn't know what $start is, since you only declared that in the starttime sub. Now if you'd do it like the following, it would print out 5:

my $start;
my $end;

&starttime;
&stoptime;

sub starttime{
   $start = time;
   sleep 5;
}

sub stoptime{
   $end = time;
   print $end - $start."\n";
}
[download]

Update: If you'd put "use strict;" in the beginning of your little snippet, Perl would warn you about this with: Global symbol "$start" requires explicit package name at test line 14.