While fiddling around enabling WebGL on Chromium yesterday (I'm now starting Chromium with –enable-webgl –ignore-gpu-blacklist, the latter being necessary because I have an ATI video card), I tried the latest Chrome release. Once back to Chromium, none of my bookmarks displayed a favicon.
It looks like Chromium keeps favicons in a SQLite database (.config/chromium/Default/Favicons). Stopping Chromium and deleting that file has made bookmark favicons start working again.