Chrome + HTTPS/SPDY can sometimes cause that to happen and it’s on my todo list to see if we can get better metrics out of Chrome. It mostly stems from the fact that we have to trust Chrome to tell us about encrypted requests (other browsers we can access the byte stream directly) and sometimes at the start of a navigation Chrome has a problem accounting for things that happen while the renderer process is starting.
There are tracing hooks at the browser level (and also the netlog) that might give us the necessary information to reconstruct the timings correctly for the missing time.