Are there any robust ways to grab records from a CSV file?

Yes, use Perl's native getline method (what you're calling when you use angle brackets on a filehandle).

To see if your discrepancy results from embedded newlines or simply from blank lines, you might try a histogram of commas seen per line.

my %lines_with_this_many_commas;
while (<$csvfile>) {   
    my $comma_count = tr/,/,/;
    $lines_with_this_many_commas{$comma_count}++;
}

print "Perl's getline counted $. lines\n";
print "with the following incidence of commas:\n";
my $PRINTF = "%10s  %30s\n";
printf $PRINTF, 'Commas', 'Lines with this many commas';
for my $n (sort {$a<=>$b} keys %lines_with_this_many_commas) {
    printf $PRINTF, $n, $lines_with_this_many_commas{$n};
}
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