I had the same problem with RoM and other stuff I recently bought (CK2, Stellaris). Manually copying all the codes from the Paradox site to Steam was quite cumbersome, but a least it worked. I decided that I don't activate the CK2-EU4 converter, so that when I figure out what's wrong I have something left that I can try to activate from the Paradox site. Then I found this thread and especially this post:
I'd also suggest breaking the Steam link on your Paradox account and re-connecting it to see if that works.
I did that and then it worked again, i.e. I was able to activate the CK2-EU4 converter.
Unfortunately the games that I bought in the Paradox store, but activated in Steam still had the orange "Activate" button on the Paradox site. Jorlem had a similar problem:
The buttons were initially unchanged, but pressing them again resulted in an error message saying that the keys had already been activated (Error code 400), and the Activate button turning into the grayed out Activated not-button. This occurred for both of the RoM products shown in the screencap above, and the CK2: Full Plate Metal product, which was one of the other two that had the stuck button. The last one, "Crusader Kings II: The Reaper's Due Collection", still has the Activate button that is pressable and won't clear, even though the product has been active since the day it came out.
Clicking on the orange buttons that already should have been grayed out lead to an error (code 400). Which is okay, since the error message simply states that this code has already been used. After reloading the page the button I just clicked was finally grayed out. So I thought to myself that I just have to click all the buttons, reload and everything should be fine. Well, that worked... unfortunately I could only click 3 buttons at a time and then had to wait for about an hour. Steam doesn't like activation requests of already used keys too much and forces one to wait. (I guess they have to do that not to be flooded by such requests.) So (mainly because of CK2's numerous DLCs) it took a couple of hours, but in the end not only all my stuff was activated but every button that should be grayed out was too.
It's not a major issue, but I think Paradox would do itself a favor by taking a look at this. After all issues like this might scare away people from using the Paradox store and from what I understand Paradox gets a little bit more money from those purchases, compared to Steam purchases.
edit: fixed some spelling errors