Now, if you want to actually explain why you think it makes sense to combine CGI.pm with interactive input...

I apologise once again, I was trying to keep it simple, reducing the problem to the simplest case...

As it is, I see more explanation is in order. I have a perl script using sqlite that works very well. Very much simplified, it looks like this:

use strict;
use warnings;

use DBI;

my @fields = ( qw/ Genus Species Cultivar Common_Name / );
my $field = get_field( @fields );
my $value = get_value( $field );

# Omitted: code to connect to DB
my $select_query = qq/ select * from plant where $field = '$value' /;
# Omitted: code to execute, fetch and deallocate SQL query

sub get_field {
  # Highly simplified for testing purposes
  return $_[3]; 
}

sub get_value {
  print $_[0], ': ';
  chomp ( my $choice = <STDIN> ); # <- Problem here!
  return $choice;
}
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...by telling us more about what you are trying to do...

I am converting this program to a CGI script. I decided to do the HTML output bit first. Of course, once I have finished, I will not be combining CGI.pm with interactive input once the development phase is finished. However, I was surprised that adding use CGI; to my code added a subtle bug that it took me a very long time to track down.

...then we could probably tell you the proper way to prevent this problem

It's all right, thanks: as I say, I've now tracked down the bug (which thanks to your explanation I accept is in my code, not in CGI.pm :) and found a workaround.