You will find that you signals and devices will automagically disappear when you leave output and inputs unconnected; particularly outputs should be connected to something if you want to observe them. I really pulled my hair out while using signal tap because all the signals (during intermediate design testing) I wanted to look at would just disappear. Then I found that you didn't need to use the signaltap "wizard" and you could directly instantiate the signaltap ip as a component directly. It's a little more trouble, but well worth it if you want to keep some signals/registers/outputs.