I use the S-Gear Scuffham Amp guitar plug in within Sonar. It works perfectly, but there is practically no visible waveform. If I zoom vertically to the max, there is something there, but in a normal view it is just a line. The audio level is perfect, and if I use exactly the same input level on my Saffire 6i6, but use TH3, the waveform is normal.

any ideas?

I don't have S-Gear, although I should, so I can't test this. However, I can't think of any reason that a plug-in would affect the waveform that is drawn on a track. 
 
Are you saying that if you remove S-Gear from the EFX bin the waveform draws correctly or are you saying that if you record when S-Gear is being used on the track that the waveform doesn't get drawn? 
 
You can click on the clip and there should be an option to re-draw waveforms. 

It's ok, I've just sorted this. Despite sounding perfect before making any adjustments, in order to have a waveform showing properly I needed to increase the input and output levels within the S Gear plug in and make a corresponding decrease to the input level on my audio interface.