Slightly opaque bug there. ;)

shift without args, in main code is the same as shift @ARGV; I'm sure we agree there. Well, when you shift the first value off of @ARGV, that changes the array, so in your second comparison, you're looking at what used to be the third element.

For example:

#perl mytest.pl sn 5

# Before anything else is done, @ARGV looks like:
# $ARGV[0] = 'sn'
# $ARGV[1] = '5'

my $based_on = $ARGV[0] ? shift: 'tp';

# Now @ARGV looks like this:
# $ARGV[0] = '5'
# $ARGV[1] = undef

my $top = $ARGV[1] ? shift: 1;

# It's going to return '1' because $ARGV[1] was undef, due to
# the first shift.
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What you should try instead is:

my $based_on = defined( $ARGV[0] ) ? $ARGV[0] : 'tp';
my $top      = defined( $ARGV[1] ) ? $ARGV[1] : 1;
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...or using shift:

my $based_on = defined( $ARGV[0] ) ? shift : 'tp';
my $top      = defined( $ARGV[1] ) ? shift : 1;
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