I made a reservation on Opentable for a restaurant that was on Groupon recently, and did so using a link on the restaurant's web site. I didn't pay attention to whether I was getting points at the time I made it, but when I went back to see if there were other reservations available at a different time (there were not), I noticed that other times got 100 points but my reservation had none. Because of the popularity of the Groupon, there were no reservations available at my time and I didn't want to cancel and take a chance of my table not becoming available to rebook, so I did without the points (since 100 points is only $1).
I checked the Opentable FAQ's and they do say that you may not get points if you do not book directly from their website. I'd seen restaurants without points before and figured it was just the restaurant but now I realize it may have been the way I was booking. I will make sure I manually go to their site in the future to get my points. I figured I'd warn others about this as well.