Hi, personally I am not very familiar with the pareja de hecho regulations but after seeing your initial question in EOS unaswered for a few weeks and Spanish being my mother tongue, I have been researching the issue on the internet.
In Spain there is no central registry for parejas de hecho. The registries are regulated by the regions (Comunidades Autonomas) and there are some regions that do not have one. This generated a problem for the citizens of other EU countries being able to obtain registration as the EU regulations on this matter provide that the domestic system must ensure that EU citizens cannot obtain double registration (for example registration with two different partners in two different registries). Under the current Spanish system, there is no guarantee that you cannot be registered with a partner in say, Andalucia, and wth a different one in, say Murcia. This had been interpreted by some Communities to mean that non-Spanish citizens could not be registered in the Parejas de Hecho registry.
Apparently a Court ruling has been issued in November 2011 whereby it has been interpreted that the lack of a nationwide regulation of the Registries in Spain should not be interpreted to mean that citizens of other EU countries cannot have access to their local registry.
The bottom line of your problem, therefor, could be that your local registry was perhaps waiting for resolution of this issue before giving you the appropriate certificates. I cannot assure you, unfortunately, whether this is really the case or not, but perhaps the above might prove useful for you to resolve the problem. I hope this helps.