I have had this problem forever, and it does not seem specific tothe version of Chrome I'm using. I've updated several versions of Chrome, and they all behave the same way. Currently, I'm running the following:
1) Norton Security with Backup: 22.5.4.24
2) Chrome: 46.0.2490.86
3) IE: 11.0.9600.18098
IE does have the same issue at times, but usually is the one I have to use to log into Capital One's site. Both Chrome and IE get "filled in" by Identity Safe, but Chrome fails Authentication by Capital One. Chrome ALWAYS fails, but IE will typically work after a re-try or two. It's frustrating. What's the sense of having the safe if it won't work? Shutting off the safe and manually typing in the id/password with Chrome works fine. Chrome on its own has no issues and I get into Captial One just fine WITHOUT the safe enabled. Maybe I should just migrate to Lastpass??