BTW, I dont see an email for the registered user either informing him about the gift certificate.

Email functionality is definitely working on the site, as other Drupal modules including Ubercart use it successfully.

In the case where as administration I directly (without purchase) create/grant a gift certificate, only one certificate database record is created but no emails are sent.

Also it does look like new user accounts are being created for the the non-registered users so it looks like we have email issue and an issue with duplicate record generation on purchase.