I've been experiencing this same exact problem for several days and finally isolated CCleaner as the culprit. More specifically, the "cleaning" of "Internet History" (ONLY) under Chrome in CCleaner is the issue. I've run numerous tests and have fully verified that this setting is the issue. As long as I leave it unchecked my Chrome settings stick with no issue after reboot (and auto-CCleaner on boot-up).
I should note this was never an issue for me in the past, until about a week ago, and I have not really added, changed or updated much in my PC, including no recent update of CCleaner or Chrome that I know of. I realize Chrome can sometimes update behind the scenes, but I don't think it did. Anyway, here are the current versions I am running of each application. I hope this information helps others, as well as assisting CCleaner in properly addressing this issue within the application.
Chrome Browser Version 32.0.1700.76 m
CCleaner Version 4.06.4324 (64-bit)
OS Windows 8.1