After some investigation, I've come across this: https://code.google.com/p/chromium/issues/detail?id=401365, which suggests chrome will throw this warning if any certificate in the chain is using SHA1 and has a validity longer than 01/01/2016.
Lo and behold:
[edit]
Apparently this only affects people who have this certificate stored.
[edit2]
This:
Chrome stores SSL certificate state per host in browser history.
So just clear browser history (Ctrl+Shift+Del), at least the following parts:
Cached images and files
Hosted app data
Content licenses
Finally resolved the issue (Source: How do I clear Chrome's SSL cache?)