After testing a few alternatives, it seems to be that the issue is with DateTime::Set->from_recurrence. Manually populating a set seems to work.

</#!/usr/bin/perl -w
use strict;
use diagnostics;
use DateTime;
use DateTime::Set;

my $date = DateTime->today();
my $date2 = $date->clone();
$date2->add('days' => 14 );
my $set1 = DateTime::Set->from_datetimes( dates => [ $date, $date2 ]);
my $iter = $set1->iterator;
while( my $d = $iter->next ) {
        print $d->datetime, "\n";
}
my $date3 = $date->clone();
$date3->add('days' => 7);
print $set1->contains( $date3 ),"\n"; # gives 0 correct!

my $biweekly = DateTime::Set->from_recurrence(
        'recurrence' => sub {
                return $_[0]->truncate('to' => 'day')->add('days' => 1
+4)
        },
        'after' => $date
);
my $set4 = DateTime::Set->from_datetimes( dates => [ $date3 ] );
print $biweekly->contains( $set4 ), "\n"; # gives 1 wrong!
print $set4->contains( $biweekly ), "\n"; # gives a warning
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You said you had a solution already, but you could create the recurring dates yourself and then it should (hopefully) work.