In X3, in the track view, when I am recording, I see the waveform in the clips. However, when I close Sonar and reopen it, the waveforms are gone. I still hear the audio, but only a straight line appears on the track. What can I do about this?

Hi profsog . . . welcome to the forum !
 
You could try right clicking on your audio clip (or use key shortcut Shift-K), then at the bottom of the window select "recompute pictures" . . . if there is still no waveform preview you may have to change the zoom factor or percentage of the audio clip display. (by dragging the vertical bar between the tracks and the clip view)
 
Also, make sure in preferences -> file -> audio data . . . that your "Picture Folder" setting is C:\Cakewalk Projects\Picture Cache (this is where the waveform displays are generated from)
 
Let us know how it goes.