Update April 8, 2016: I decided to give Amazon another try. It has been over a year so they must have sorted out the issues from earlier right? I did some research and discovered that Amazon will not reinstate a closed account for any reason so I set up another account and put ads on two of my blogs. Several weeks later they contacted me to say that they couldn't find my website and they closed my account.
40,000 other people can all find my website so I don't know what their issue is. The entire set up is starting to feel like a scam. You set up an account, wait a few weeks and then then they close it for some odd reason like "not enough people are clicking on the links."
Unfortunately the Amazon Associates system has not changed much. It's just as unstable and unreliable as it was the last time I tried it. If you are looking for affiliate marketing options then do yourself a favor and skip right past Amazon. It's not worth the hassle of setting up only to have to take it all down again a few weeks later.