Repro steps:
1) Open the project and main.scene in it
2) Load RenderDoc on the Game View
3) Press play and capture the frame with RenderDoc icon
4) Also, notice there are a lot of log messages in the console of Unity
5) In the RenderDoc investigate the captured frame's Event log
6) Notice, that there are no calls from scripts captured (in this case -no Shader Dispatch Calls from Update())

Reproduced in: 5.4.0b2; 5.3.1p3
Cannot load RenderDoc in earlier versions