I have my developer working on this.
it is not an easy one to investigate. We build the portal to replace www.salaro.com and add a lot of new fanctionalities by adding new modules. Store is Portal Store which works fine. but we have not touched the core. so as DNN upgraded from 4.4 to 4.5.x we had no issue.
We lost the Registeration on 4.6 and 4.62 did not solve it.
unfortunatly becuase we thought the problem was skin and skin token. we continued working on the site for nearly one months. adding skinpackages etc...
So now to revert back to 4.5.x which we could as we have the DB and the backup, but this is difficult as we would loose a month of efferts.
One thing I am going to explore is the fact that you said that the
"registration has changed in DNN 4.6 due to the new authentication providers, you need to have a look into the changes of the methods you are using."
This makes me think that if Portal Store is using a older Autentication methods. this could be causing the conflict.
At the moment - if I test the store. and try and buy a product, it will not allow the purchase as the store comes up with the message that can not register you to proceed with the purchase.
I have sent Richard an email. He has been extreemly helpful in the past.
Regards
Salar