Im having the exact same issue as this: https://code.google.com/p/chromium/issues/detail?id=475108 It should be fixed since ~ 1 month, but im still having the problem on Chrome Version 46.0.2490.80 m, using Windows 8.1 64 bit.
I tried everything i found in the web, like deleting a thumbnail - restore it - reboot. Or what is described here: http://www.howtogeek.com/howto/34690/refresh-most-visited-page-icons-in-google-chrome/
Now after messing around the whole day, im kinda giving up and ask you guys for help please. The error in the console looks like "GET chrome-search://thumb/XYZ::ERR_FAILED Failed to load resource"