Instead of presenting us with bits of isolated code, please provide an SSCCE that reproduces your problem and is written in such a way that we can run it and help you towards a solution.

I cannot reproduce the problem myself...

To try and get to the bottom of the problem, I have written this script:

#!/usr/bin/perl -T

use CGI::Carp qw(fatalsToBrowser);

use FindBin qw($RealBin);
my $safepath;
BEGIN {
    if ($RealBin =~ m!^(/home/username/uk/www)!) {
        $safepath = "$1/../lib";
    } else {
        die "Illegal use of software - visit www.example.com to use th
+is site";
    }
}
use lib "$safepath";

use Site::HTML;
use Site::Wayfinder;
use Bod::CRM;

use strict;
use warnings;

my $crm = Bod::CRM->new('test');

print "Content-type: text/plain\n\n";

my $db = '...';
my $un = '...';
my $pw = '...';

#####  Uncomment one line #####
#my $dbh = DBI->connect("dbi:mysql:$db:localhost:3306",$un,$pw) || die
+ "DB ERROR: " . $dbh->errstr;
my $dbh = $crm->db;

$dbh->do("CREATE TEMPORARY TABLE Temp_Test (
            idTest   INT NOT NULL AUTO_INCREMENT PRIMARY KEY,
            fname    VARCHAR(40),
            nname    VARCHAR(40),
            sname    VARCHAR(60),
            email    VARCHAR(100),
            altEmail VARCHAR(100)
        )
        ENGINE MyISAM");

print "ERROR: " . $dbh->errstr if $dbh->err;

$dbh->do("INSERT INTO Temp_Test (fname, nname, sname, email) VALUES ('
+Ian', 'Bod', 'Boddison', 'me\@example.com')");
$dbh->do("INSERT INTO Temp_Test (fname, nname, sname, email) VALUES ('
+Boomer', 'Boo', 'Dog', 'dog\@example.com')");
$dbh->do("INSERT INTO Temp_Test (fname, nname, sname, email) VALUES ('
+Oi', '', 'You', 'you\@example.com')");

my $query = $dbh->prepare("SELECT * FROM Temp_Test");
$query->execute;
$, = ' - ';
while (my @row = $query->fetchrow_array) {
    print @row;
    print "\n";
}

my %data;
$data{'email'} = 'dog@example.com';

my $crid = $dbh->selectrow_array("SELECT idTest FROM Temp_Test WHERE e
+mail = ? OR altEmail = ?", undef, $data{'email'}, $data{'email'});

print "ERROR: " . $dbh->errstr if $dbh->err;

print "\nCRID: $crid\n";
[download]

So what I have done is to go back to the code that is behaving strangely and double check it.
It has been stripped back to bare minimum and the strange result still happens:

#!/usr/bin/perl -T

use CGI::Carp qw(fatalsToBrowser);

use FindBin qw($RealBin);
my $safepath;
BEGIN {
    if ($RealBin =~ m!^(/home/username/uk/www)!) {
        $safepath = "$1/../lib";
    } else {
        die "Illegal use of software - visit www.example.com to use th
+is site";
    }
}
use lib "$safepath";

use Site::HTML;
use Site::Wayfinder;
use Bod::CRM;

use strict;
use warnings;

my $html = Site::HTML->new;
my $wf   = Site::Wayfinder->new;
my $crm  = Bod::CRM->new('test');

$html->head;

my $logbox = 'log_login';
$logbox = 'log_fpass' if $data{'command'} eq 'fpass';

# Reset password
if ($data{'command'} eq 'rpass') {
    my $test = $crm->db->selectrow_array("SELECT idPerson FROM Person 
+WHERE email = ? OR altEmail = ?", undef, $data{'email'}, $data{'email
+'});
    
    print "<p>TEST: $test</p>\n";
    
    my $query = $crm->db->prepare("SELECT idPerson FROM Person WHERE e
+mail = ? OR altEmail = ?");
    $query->execute($data{'email'}, $data{'email'});
    my $crid  = $query->fetchrow_array;
    
    print "<p>CRID: $crid</p>\n";
    exit;
}

__END__
[download]

The output is:

TEST: 0

CRID: 1
[download]

update:

Just to prove it is not something that is happening in Site::HTML->head, I have changed:

$html->head;
[download]

#$html->head;
print "Content-type: text/plain\n\n";
[download]

<p>TEST: 0</p>
<p>CRID: 1</p>
[download]

"I cannot reproduce the problem myself..."

Why not? Please explain.

"To try and get to the bottom of the problem, I have written this script:"

But why post it here. It's littered with all sorts of things unrelated to the base problem which, until we know more, would seem to be database-related. There is taint-related code, web-related code, and three non-CPAN modules about which we basically know nothing. This is not an SSCCE.

I wrote a succinct test and suggested you try it: that doesn't appear to have happened. At the time of writing, you hadn't told us what database you were using. I chose SQLite because it's common and easy to use. If you don't have it, you should be able to write something equally simple with "dbi:SQLite:..." replaced with "dbi:mysql:...".

"The selectrow_array function should not be able to return zero when zero does not exist anywhere in the idPerson field of the database."

What's the basis for that claim?

In "DBI: selectrow_array", there are three examples with '@row_ary = ...'; none with '$some_scalar = ...'. It talks about how calling this in a scalar context can be handled differently depending on the driver being used. It ends with "... you should exercise some caution if you use selectrow_array in a scalar context, or just don't do that." [my emphasis]

Perhaps what you're seeing is something akin to:

$ perl -E 'my @x = (); my $y = @x; say $y'
0
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If, after writing an SSCCE and perhaps resolving issues, this still fails in your main application, I would suggest the next step would be to write a /path/to/Bod/CRM/NN-selectrow_array.t and compare '$dbh->selectrow_array(...)' with '$crm->db->selectrow_array(...)'.

My code shown so far uses Perl(5.34.0), DBI(1.643) and DBD::SQLite(1.66). I don't have DBD::mysql installed and I haven't used MySQL for about 20 years, so I can't really help you with that.

— Ken

It's littered with all sorts of things unrelated to the base problem which, until we know more, would seem to be database-related. There is taint-related code

Those unrelated things have to be there.
The problem goes away if I turn off taint mode...