Putting everything all values quotes is not correct. It's not enough to convert strings into SQL literals, and it's just plain wrong for numbers. You should be using replaceable parameters aka placeholders. See the DBI docs and PerlMonks for more info on these.

my $price = '23,356.00';
my $itemref = 'S10099';   

my $query = "UPDATE items SET price=? WHERE itemref=?;";  <---
$sth = $dbh->prepare ( $query );
$sth->execute ( $price, $itemref );                       <---
$sth->finish ();
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Not saying this will fix the problem you asked about, but it might. It should be done either way.