I would say that about 1/3 of my purchases thru MyPoints do not track automatically. However, I have found that their customer service has always been very responsive when I write to ask them about missing points.
One thing that I have found to be very helpful is to save every confirmation email from the merchants so that a copy of it can be sent to MyPoints is the points fail to credit. They can track the purchase more easily that way.
I have also found that initial replies from MyPoints Customer Service is almost always a canned response that tells me to wait 20 business days following the purchase in order for the points to credit. That canned response will also have a tracking number. If you include that tracking number in subsequent emails, the problem is more easily resolved. If the 20 business days have already passed, I just email them back, with the tracking number in the subject line, and ask for my points.
As far as using special codes (like Reflect.com's free lipstick code, etc.), I usually copy the code by highlighting it and then right clicking on it and choosing *copy*. I then right-click on the spot to enter the code on the vendor's site and click on *paste*. Most of the vendor codes are either in the email that MyPoints sends to you or are on the jump page that you get when you click on the vendor's banner at MyPoints. In rare cases, it willl appear in a pop up.
Thanks! 
