It’s nothing to do with my systems performance, which is actually pretty good. (i7-3820K & GTX 560 Ti ‘448’ Edition).
As I said above, if you uncheck all of the flags in the ‘Usage’ section, the problem seems to go away, and it won’t compile until you recheck them and save the shader. Changing colours in parameters causes a recompile though, which is utterly frustrating. Iteration time in the Material Editor in general is pretty poor, and we never had the issue in UE3. What’s worse is when it does compile the shader, you are presented with the default material, making it incredibly difficult to compare your changes to the previous ones anyway.