I assume you are trying it with a MobilePass :)

Italiarail can´t proof the Mobile Pass numbers Bestway is to contact Customer Support as they can give you a Standard Passcover number that will be recognised by Italiarail.

No I have PaperPass… 

Then please contact customer support to receive a pass cover number.

I got the same issue (although I have a Mobile).
I contact the customer support of Interrail, let’s see how it goes.

Side question : is there another way to book “frescia” trains than ItaliaRail ?

At the station, also outside of Italy. I know Deutsche Bahn can do it, possibly SNCF too.