For me, when I tried linking my 3DS when the update first came out, nothing showed up on my points..
So that led me to try and unlink and relink maybe like twice or so?
It still had not shown that it's linked on Club Nintendo, and I googled it and saw that other people couldn't successfully link their system.
I think a few days later, I checked again, and I had 80 more points than I did before. I checked the log thingie, and voila, I was given 40 coins twice. Except my system still isn't linked.. I have unlinked and tried linking it again, but no more points, and no successful linkage either..